Second and third layer can be done with events and scripts that let you use the region layer to give you an extra layer. Honestly though, I don't think really going to the region layer is even necessary. People exaggerate the need to stack things on top of each other to that degree. And Ace makes cosmetic eventing much more viable as it cuts lag down so much its a nonissue. Unlimited tilesets is really a red herring, because I can't think of a legitimate case anyone would have for using the full A-E tileset in ONE MAP. Also XP lagged when you tried to use "unlimited tilesets" so really there was a practical limitation there anyway.
The autotile format of XP is the one thing I think you have a good point with, but even in that case, I think people stress how necessary it really is. And even with that, I can get around some of the limitations with tileb-e layer tricks combined with shift clicking.
EDIT: I'm not denying that XP has a better autotile format, and that the layer control isn't awesome. IT REALLY IS, I'm just saying that Ace outdoes it so much in every other area, that layer control+autotile format are the only two things I see XP as really better at, so IF we were going to do an update (which I'm not speaking as a rep here, so don't try to make something of this more than a fan rambling) it would be better to give Ace layer control and better autotiles than to try to bring XP up to Ace.
If you want to get into Events being a third layer, then RMXP has 4 Layers. If you use the default VX/Ace tilesets, you don't need more layers or tiles than what is given. When you start moving onto different tilesets that use different proportions, you start to run into a problem. For example, without 2+ upper layers, you can't have trees that are 5 tiles wide and 6 tiles tall overlap in any particularly interesting way. You could make more tiles, and more tiles, and more tiles for all the different combinations but you eventually run out of tiles. You can only add so much more from events. Then you are left with Pre-Rendered Mapping.
Also, while Cosmetic Eventing is great in small doses, when you start covering half to two thirds of your map in events just to achieve a certain level of aesthetic, you are now running into serious lag problems just from events. Not to mention that is significantly less room on your map to place events that actually add to gameplay.
Yes, XP lagged when you used massive tilesets. Pretty horrendously actually, but I have overextended the A1-5BCDE tiles many times in trying to achieve an effect I wanted. I also don't consider A1-4 to be usable since the 64x64 autotiles are almost too small to even make useful
autotiles out of. The problem isn't with shift clicking and "tricks", it's that the corners of the tiles are 16x16 tiles. You probably understand this since it's a point you agreed with me on but in a system of 32x32 tiles, why would any one tile be less than that? The corners are 16x16, the edges are 16x32 (and 32x16 respectively.) This not only creates an unattractive block-y effect (which works fine with the default tiles, I guess.) but it makes the autotiles almost impossible to create new tiles with in any style other than the Dragon Warrior-esque style that Enterbrain has attempted to force feed us through the RTP and mapping system. This is a MAJOR issue for anyone trying to use the software
as it was intended but still utilize a different style.
There is only so much space on A5 you can use to create non-autotile ground tiles, and then you are forced onto B-E which eliminates your ability to layer tiles, except with events which is not an option I agree with.
Edit: Since I was oblivious to your last line and now realize you didn't need further persuasion, I'll add that I also agree that VX Ace does everything better than XP except mapping. Yet, Mapping is one of the most important things in a 2D RPG. It's not something that can just
be worse because everything else is better. Enterbrain had a chance already to fix the huge step backwards they made with VX, with Ace. They chose to focus on one small thing (tilesets) and not take the effort to remake the mapping system or implement XP's mapping system. This was a huge oversight.