What I Wish The Puzzle Creator Could Do...
Ok so most of what you said seems unnecessary. If you want to make something look good, use a better tool. I rarely use the puzzle editor because I would rather draw on paper first. The editor is my second tester for more complex puzzles.
I agreed with some of your points like holes in glass and moving the antlines, but there are definitely alternatives - even with the puzzle maker. As for crossing confusing indicators, try splitting up your puzzle or think up a more intuitive design with re-use of elements.
One thing that got me was this:
Perhaps you don't understand how animations work. Stopping an animation half way through would cause a number of problems including visual glitches, sound errors or sudden stops. A full animation for each stop of the panel would be easier than using specific timing to 'pause' as a number of logic entities would be needed to decipher when the panel is open and would have to calculate what precise time it needs to stop.
Would you like to figure out the exact timing to stop the panel at an exact angle? Good luck.
You could do it with a func_rotating, like with the rotating portal gun stand. That's precisely timed.
EDIT: Tell you what, what if I gave you a panel that rotated as long as it was powered? With the FGEMOD and BEEMOD you have all the necessary entities to time it correctly. 
So you are looking for an easy MAP maker not a PUZZLE maker, because right now you have an excellent PUZZLE maker. Hammer is not as difficult as you might think, it takes about a week to really start using. And its going to be your only option for making ascetically pleasing MAPs
as for the smaller voxels, LP is right, there is no need to implement this, it would just cause a whole lot more problems for puzzlemakers... it is however not impossible, I almost decided to scale the voxels down to 32 quare units for the BEE2, it however would take a re-writing of the scrips, and a lot of work for august adjusting the size of models, and for nearly no gain.
I agreed with some of your points like holes in glass and moving the antlines, but there are definitely alternatives - even with the puzzle maker. As for crossing confusing indicators, try splitting up your puzzle or think up a more intuitive design with re-use of elements.
One thing that got me was this:
Perhaps you don't understand how animations work. Stopping an animation half way through would cause a number of problems including visual glitches, sound errors or sudden stops. A full animation for each stop of the panel would be easier than using specific timing to 'pause' as a number of logic entities would be needed to decipher when the panel is open and would have to calculate what precise time it needs to stop.
Would you like to figure out the exact timing to stop the panel at an exact angle? Good luck.
I think what I am trying to say is why use something that is clearly overkill for most players? Instead, for most of us, we get what seems like a half-assed editor. Why not meet in the middle? I honestly didn't think the editor would be released as fast as it was. It's good, yes, but I think it needed more time to be refined and polished.
Not exactly. I'm saying why don't we have a beefed-up version of the current puzzle creator? This doesn't have to be all or nothing. I'm seeing three levels of editing control:
1. Basic (current release of the puzzle creator)
2. Advanced (what I'm suggesting)
3. Expert (Hammer)
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Single Player Tests - Excellent Partnership (Coop) - Single Player BEE Mod Tests
Not exactly. I'm saying why don't we have a beefed-up version of the current puzzle creator? This doesn't have to be all or nothing. I'm seeing three levels of editing control:
1. Basic (current release of the puzzle creator)
2. Advanced (what I'm suggesting)
3. Expert (Hammer)
no, right now you have a full puzzle maker for all users.... the things you are suggesting are mostly aesthetic which are not nessesary in PUZZLES. Valve gave you a full PUZZLE maker, they are not going to release a crappy half version of hammer. Hammer is not for Experts.... Hammer is just an Advanced editor. Coding Hammer is for experts. If you want to make puzzles use the PTI, if you want to make real maps, use hammer. dont complain thats its too hard or you dont have the time, the fact is that you just want an easier way to do something. and you want other people to make it easier for you, when really its not all that hard to begin with.
Dont be that lazy person, its like the common American "I dont want to make dinner, so I'll just get some fast food"... soon that lazy American is fat, and is online searching for a faster way to get thin because they "don't have the time to go to the gym, or eat healthy food".
Hammer takes no more than a week to learn, its way more powerful than any handful of PTI mods. it is also a useful skill if you ever plan on doing any real game design.
Also, don't forget that everyone on this site was at one point a beginner, we know how ridiculous hammer looked before we learned it, and in retrospect, it was really easy to learn.
So stop trying to take the quick way out, and watch these tutorials, follow along and once you're done, you'll be able to make a better looking map, faster than the PTI can generate one.
http://www.tophattwaffle.com/tutorials/
https://developer.valvesoftware.com/wiki/Main_Page
I spent the few weeks between when I beat P2 and when the Portal 2 Authoring Tools came out reading through everything I could find on the VDC. I became an awesome mapper in theory, although I still don't know how to use the clipping tool properly. 
Hammer doesn't take too long to learn, the big part is learning all the entities and what they do. At first you can just use brushes and func_instances from the p2editor folder. That's enough to build (almost) anything you can make in the PTI. Then you can try using more logical entities and such.
Dont be that lazy person, its like the common American "I dont want to make dinner, so I'll just get some fast food"... soon that lazy American is fat, and is online searching for a faster way to get thin because they "don't have the time to go to the gym, or eat healthy food".
Hammer takes no more than a week to learn, its way more powerful than any handful of PTI mods. it is also a useful skill if you ever plan on doing any real game design.
Also, don't forget that everyone on this site was at one point a beginner, we know how ridiculous hammer looked before we learned it, and in retrospect, it was really easy to learn.
So stop trying to take the quick way out, and watch these tutorials, follow along and once you're done, you'll be able to make a better looking map, faster than the PTI can generate one.
http://www.tophattwaffle.com/tutorials/
https://developer.valvesoftware.com/wiki/Main_Page
You just don't get what I'm trying to say. The authoring tools were released weeks later after Portal 2 was released. There was quite a response from the fan community creating their own puzzles with the tools. That's why the puzzle creator was made. My concern is that it may have been released too soon; it just looks rushed to me when more could have easily been done to it. Hammer is designed to create maps for use in games that use the Source engine to run. The puzzle creator is within the scope of Portal 2. Its focus is purely for test chamber creation and nothing else, a perfect way for me and many other players to get test chambers from paper to game very easily. With your logic, Valve should not have made the puzzle creator in the first place. I'm just wondering why it is so basic. How I question it is by sugggesting things it could be doing to hopefully meet middle ground and make it more robust and rounded, but not to the extent of Hammer. It's not that Hammer is hard to use but really it is too complicated. That is why I say Hammer is overkill for what most players want to do with Portal 2. If some players want to do more than that, like you, then Hammer is the right tool. If you prefer it over the puzzle creator, good for you. If you are basically just going to keep suggesting Hammer as a reply for every post I make in this thread, don't bother commenting because it is not contributing to the topic at hand. I didn't want this discussion to turn into something like that.
Plus, every suggestion I made appears in a test chamber, not the entire map, throughout the single player and coop campaigns at some point.
Why does Hammer have to do the aesthetic and timing tweaking parts of a test chamber? Why can't it be the puzzle creator as well? It's not like I want to change themes or something (decay, 1940s, Wheatley, etc.) which would be a better reason to use Hammer.
Click my Steam Profile image to view my Portal 2 Workshop!
Single Player Tests - Excellent Partnership (Coop) - Single Player BEE Mod Tests
It doesn't. Most of the first maps made by people look terrible, and IMO, hammer makes things simpler. I don't need to scale my chamber 4? as large to make it proportional with a 32 unit block. I can simply make one like that. *snap*. Isn't his exactly what you were referring to? You want to fix the silly zig-zag indicator lights. Make them in hammer, or even export it. A well exported map can make a map better. (And in some cases, worse). Hammer isn't difficult to learn, and I don't think people really care about aesthetics on your first map. No matter how impossible it looks, hammer basics are just remembering what does what, and where on youtube you can figure out how to make things your not sure of yet. VALVe's puzzlemaker is great. I have seen amazing maps, and there are always things people will want added that will do more damage than good for the portal community. BenVlodgi has made the best points here.
Nope, still not getting where I want to go with this. Stop trying to convince me that Hammer is what I need to use to achieve what I want to do. I'm sure Hammer is an awesome tool, but it is overkill for most people, and the puzzle creator removes the tediousness behind it but at the same time makes it too basic. I wish the puzzle creator could do this instead, because, if Valve developed it differently, it could easily be done. I wanted to discuss, not achieve the results I'm looking for, without bringing in Hammer to the discussion, but I guess I can't have that kind of a discussion here.
Click my Steam Profile image to view my Portal 2 Workshop!
Single Player Tests - Excellent Partnership (Coop) - Single Player BEE Mod Tests
Well the guys at Valve think its perfect... perfect for roughly smashing out new puzzle ideas, which was their goal from the get go. I know because I ask them if they are adding new features, and they ask me... "what more could we possibly add?"
and I have nothing to say, because there isn't anything to add... They spent many more months than you know working on this. They only announced it once it was actually to a relatively finished state (which beta testing proved wrong)
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Also fun-fact there is no Portal 2 team at the moment, everyone has moved on to new projects, so I wouldn't be expecting any Portal related DLCs any time in the next few months.