If you take a look at my game, it looks like something one could make with more ease on RPG Maker, so why did I take an extra step and remade everything on Unity?
1. 3D, not a problem if you want a fully 2D game tho.
2. Language preference: RPG Maker used Ruby and now it uses Javascript but unless you plan to make something pretty standard or use plugins from other people, if you want your game to be unique, you will need to code yourself and that requires you to be comfortable with a certain language... In my case, I like C#.
3. Simplified for ease of use: Many things are too simplified to make the engine easier to use for beginners, more often than not you have to fit yourself to the engine limits... Sure, you can code a pixel movement but I am not even sure if you can recode the collisions.
Collisions are, of course, just an example... In RPG Maker XP you had to literally hack up the dll to get a different resolution, you can't have as many layers as you want (just 3,4 if I remember correctly)... My game uses 8 layers and some of them are dynamic as in they move down or up depending on the player's position.
4. Sometimes it is more work to get rid of all the stuff you do not need and shape the game on your needs than remaking the same features elsewhere.
You can notice that in those RPG Maker games where there is HP, MP, even elemental protections but not even a single fight.
Some devs put a few fights in, totally forced, only to motivate their presence.
Those are the main points I can think about right away, there is probably more.
Another thing to mention is that Engines like Unity or Ren'Py have *many* features out of the box but an empty project feels like... An empty project whereas an empty RPG Maker project has all those RPG Features displayed unless you take that extra effort to erase/hide the.
RPG Maker would be great if you want to make a final fantasy/Dragon quest porn but if all you need is a 2d top down rpg, there's probably a better solution out there.