Have you ever worked with stencyl?
I once worked with a team that wanted to make a mobile game and used Stencyl (I'm working outside the RPG Maker scene as well). Said team ran into problems early on because they wanted to make an RPG, but the engine barely managed to handle a cutscene, yet alone a combat system that offers more than just attack and defend commands.
Stencly is primarily for mobile games, and mobile games have very low memory available, not to mention mobile games must be small in filesize because it's all distributed wireless, and nobody wants to wait hours just to download a 99 cent game.
Maybe it's a different case with a custom engine, but at least with Stencyl, it's not possible to make large levels or more sophisticated mechanics. It's no understatement to say that you can only make NES-like games in terms of scale with it. If you wanted to make an oldschool platformer, that's fine, but anything larger than that is not possible with Stencyl.
Unless you want to release the game on mobiles, I suggest using another engine. But if you already have a good plan and enough experience with the engine, I'm willing to give it a shot.