What kind of issues usually come up? I'm just curious because the only RPG Maker game I've played for any length of time is The Tiamat Sacrament, and I really like the design and the mechanics in that one. It's designed where each character has a different mechanic for learning and using skills, and they all have powers that interact with the other party members' abilities so that they can only fight to their fullest potential by actually working as a team.
Honestly, when we demo a lot of people's games we usually don't last too long because the grammar/spelling is so ridiculously poor. So, even if there have been some games with decent ideas and interesting battle mechanics we never see them because we're so quickly turned off by the presentation. If there are misspellings left and right, awkward sentences and grammar mistakes, we're less likely to give the game a chance. It's just offensive.
Anyway, when we do find something that we can tolerate for more than a half hour we've found that a lot of people (not everyone) use the default damage formulas and the preset item/equipment database stuff. It's like no one cares enough about the "backdoor" work because it's not fun, for most people. There's nothing glamorous about programming stats or balancing a game. I think most projects (especially if it's one person) don't go anywhere or offer anything worthwhile because no single person (in most cases) can handle all aspects of a game. Fortunately, my brother is our "back office" kind of guy and he's come up with his own damage formulas, level growths, etc. From what we've experienced and researched in this (RPG Maker) community is that most people value visuals, scripts made by others, imported assets/tile sets, among other things...but they forget the rest!
I could go on and on about this RPG Maker/Indie scene, but I don't think this is the thread for it. I'll just leave it at that, for now, hah! =D