Seriously, why is there a layer limit to begin with? The only thing you need is Map View, and Event View. You should be able to add as much layers as possible and obviously you would then need to create your layers accordingly. Almost no tile editor even has layer limitation anymore, it was only a limit 19 years ago do to hardware limitations and I'm sure ascii based everything on what the average person has not someone like me who buys server grade hardware for reliability. There's having the fastest but there's also having the most reliable, nothing says more awesomeness like 2 CPUs!
Enterbrain really does need to release a universal type of engine, you code it, here's RGSS4, go at it! Honestly I actually found parts of Action/Indie Game Maker quite useful but that lack of actually eventing/programming the game drove me nuts! Seriously not only giving IGM Rpg Makers event system, RGSS4 or better yet javascript, python, boo, or lua would make the engine very compelling for 2D games! I do believe particles are needed in games but instead of just having an editor just make an api for it and let the developer of the game control how his/her particles should work. Yes, most modern engines even Unreal and Cryengine have particle editors, but that's in a 3D space, 2D is where Enterbrain should focus. I do believe Enterbrain put more thought into RPG Maker than Mark did in Game Maker however, Game Maker has none of the limitations that RPG Maker has and one of the big ones is the Map editor it's free aspect! But it does allow you to change the tile size on demand, While tilesets are standard at 32x32 no reason to lock it down and having to rewrite a large portion of the tilemap in RGSS just to change a few dimensions! This should be something the user can change, heck IGM has it and because I personally think Ace is what VX should have been but missed the calling when it came to free aspect mapping.
Also you guys should note Battle Animations, why isn't there an editor to animate your sprites the way you want to? You can animate your battle animations the way you want but not the most import you characters movement animations!