Well, I must say most important things were already said in here. As for me, I'll just add a bit from myself.
Pointless walking around city, especially when the game doesn't give You any map or hints where's what/who. Can be quite annoying. Was it Incest Story 2 in which You had to make some money to pay the rent, visit aunt etc. but nobody told You where's what? Not intentionally You walked into something You didn't wanted to, beacause You didn't know where You are and time advances. Kind of ruining feeling of control.
Fights. Don't get me wrong in here, I enjoy good old turn based combat, but, if the enemies are respawning every time You leave location (by accident, let's say), when You're back You have to redo a lot of fighting just to explore and check if You didn't miss anything.
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is great example, I was so tired of these repetetive fights, few times I almost deleted it. Especially in the beginning, when You're weak and they're taking few turns to win. Quite annoying.
QTE and obstacle courses. I, fucking, hate them, not only in RPGM but generally. Character movement in these games is specific, so You're not always ending up where You wanted to be, so avoiding some damn flames, guards, wolves or different crap at some supernatural speed makes me wanna break my keyboard.
Sound balance. It may be just my personal issue, but in every RPGM I can't seem adjust the volume of music and sounds without system sound mixer, even on 20% they're damn loud, every other game, movie and music seems fine. I think the issue is on me somehow, but hey, it also annoys so I mentioned.
Interface. Last but not least. There's so much clicking when You want to check Your journal, stats, items, save, load... It would be so awesome if someone could just fix this. Yeah.
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actually improved in this aspect but not entirely.
So just to quickly summarize: there are some annoying elements of gameplay in RPGM, but, like someone earlier mentioned, it mostly depend on design, so it depends... It have to be emphasized here that there are still very good RPGM games that deserves praise.