So, now I've beaten it, and except for that jelly hiccup, I didn't have much trouble until the final boss. That one was tricky, but in a good way (it's the final boss, after all), though I had to retry it at least half a dozen times. Towards the end, it got really frustrating because I had to do the same starting steps over and over again manually, and the RPGM interface makes it easy to make mistakes (e.g. casting a buff on an ally instead of selecting him for the next action). That gave me an idea, however: I think that this game would be much better off as a programming game, where you would select your weapons, write out a sequence of actions, see how far it gets you, and debug it as you go.
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That would actually work really well. I kinda love your idea!
Thing is, if I were to make a full game with RPG Maker, I would make it so long that you would get very used to the interface. It would also reach a point where the fights, although increasingly complex and hard, would have much more room for player creativity rather than allowing for 1 or 2 different answers. And you would come very naturally to these solutions due to being very used to the main mechanics.(Which isn't to say there wouldn't be new temporary mechanics unique to each area.)
I don't think that having many solutions is a problem for a programming game. The last one I played, Opus Magnum, had countless solutions for every level, and it was part of the appeal of that game. :-) I think the real problem would be implementing the programming game controls and mechanics in RPG Maker. From what I've seen in my time with it, it is not particularly flexible in regards to the interface unless you go really deep into scripting.