here, I will expand on why I don't particularly find battles in rpgmaker engaging. Needless to say, this is my personal opinion, and I don't believe I represent a meaningful number of players or anything. But I've been playing RPGmaker games for like 13 years and I think that allowed me to see when things work in these kind of games, and when they don't.
First, turn based fights are outdated. It doesn't really feel engaging to chose options from a menu and see the sprite flash white for a second before proceeding. This is the main reason I think random encounters are absolute shit. And, god forbid, I will definitely drop any fangame that forced me to grind in order to progress. You are forced to lose time fighting a meaningless entity for NO reason, hindering the exploration, which is the main drive of these games.
If you are planning to do battles on real time, *then* I could see some potential to engage the player more. This would be much more meaningful than forcing people to use easyrpg and x10 the speed to skip the brainless default mechanic. Yume Nikki had the rain / snow effect that needs to be used in order to put out the fire in the mall. In a sense, a "boss fight" that requires you to, I don't know, do certain things in order to weaken it then let the other character finish the boss (as anon 2 suggested), that certainly could be very entertaining. The only potential "bad" thing I see with this is that you'd definitely be shoving down more story than is common in fangames. But, while ambiguity and theorizing is nice, it's been so overdone at this point that trying something new would be refreshing.
With all of that being said, I think you will need some clever ideas and think these battles thoroughly if you want to make them feel more than some tedious gimmick. If you had some ideas in mind, please do share them, so we have a better understanding of what you'd like to see or do in fangames.