I personally think in this day and age the user should set what he wants their sprite sizes to be, tile size, and so on. IGM sort of got this right that it allowed you pick 8x8/16x16/32x32, and sprite sizes wasn't a limitation as long as they were formatted correctly.
RGSS/3 is good, however the map engine really does limit on how complex you want to make an action battle system, and those are the types of battle systems I prefer to code.
There is nothing wrong with tile based mapping but tile based collisions is pretty old school and was actually just an easy way of doing collisions without creating custom collisions for every object and character on the screen. That's actually something I really enjoyed in the recent release of Unity3D! I think RPG Maker should stay 2D but should allow some sort of 3D build into the engine and could be toggled without cookie cutting it with RGSS.
I also think the way charsets and sprites in general is outdated, it was fine with 2k/3 back in the day but when you want to do really complex animations you're limited unless you write a script for it, the editor should allow you to create your own animations and just call them. You can even have basic pre-settings like idl, walk, and the user can add run, fly, jump, punch, kick, and so on.
I quit using RPG Maker for my projects a long time ago due to these limitations, now these limitations are mainly for action based rpg's where a character will have more than just 2 walking frames, he could have as much as 8! That's actually easy to script but I think the user should be able to create his animations directly in the editor and it solves "do I have to edit this again for it to be smooth?". RPG Maker is a fantastic little program but it's pretty limited, IGM would be nice with even RPG Makers event system and RGSS but without it's map limitations, sprite limitations"without scripting", and would allow the user to create the action based rpg he or she would like.
IGM was a neat idea but it failed mainly because you really couldn't code and that was my gripe with it, would have been neat to actually script! JS, Boo, Ruby, and Lua would be fine for 2D games but I really think Lua is a much better option for 2D as it's basic but also complex at the same time!
RPG Maker does get the basics down, can do more with scripting and personal touches but I would actually like those features added to IGM, and an actual event system would have been great! IGM really just felt like a rushed product to compete with Game Maker which it sadly does not.
Game Maker is actually pretty "perfect" in the sense the user creates the game from scratch using the Game Maker language which just feels like a cookie cutter version of delphi but that's besides the point, the editor is basic but it's all that's really needed for 2d games, unity3d goes over the top but it's mainly a 3D engine but recently 2D tools were added which are awesome!
Ease of use is one thing, that's fine if the editor is easy to use but doing so actually causes limitations, create the commands, let the user decide how he wants the game to look and play, have a powerful event system, let the user have the power of code, and you should have a winner. Look at Game Maker, and Unity3d "with it's 2D tools", that's what the next IGM/RPG Maker should be going towards.