No, you decide on which game engine you use before you invest years of your time making the game.
I said practically the same thing in the next sentence... ;-)
But I also wanted to point out the lack of evidence that the current choice of engine is hampering views/plays of the game, since there is no prototype available yet. What I did not know, that there never was one uploaded apparantly. Only if you have a prototype and get backlash for choice of engine, one might consider a change of engine because of that. But that point was not even reached.
many of my favorite RPGMaker games either heavily customized the combat or left it out entirely.
Same. So bascially we both do not like "rpg maker" games. To be interesting to us they have to shed away things that are typical for rpg maker games and they might as well just not advertise the engine at all, because it might invoke the wrong expectations.