Hm, personally, I don't think any ROM hack can top a RPG Maker XP game like Reborn, but there are some decent ones that don't have the generic plotline:
Pokemon Snakewood: Okay, this game does have some faults like the tile errors, the fact that all three starters suck in this game, and the artificial difficulty (mainly because you're almost always below the level of Gym Leaders or even random Trainers, but the plot is actually decent. It takes place in Hoenn facing a zombie apocalypse, and you have to find your brother (the Champion) and Professor Oak's daughter (May). I haven't finished with it, since I have no clue what to do after getting the Fortree Badge, though.
Pokemon Dark Rising: Again, if you can handle the artificial difficulty, the story is (from what I've heard) great. However, I, like many others, never finished it because only one of my Pokemon was at the same level as the Trainers, while all the others were still struggling in their 20s.
Pokemon Gaia: I haven't actually played this one, but I hear it's wonderful, especially due to Gen 6 mechanics, although I don't know much about the plotline.
The last two are FireRed hacks, but they're still playable on the GBA emulator.
I also suggest the increased difficulty games like Fire Red Omega: they're like the original games, but better due to Pokemon getting buffs and real increased difficulty (like Reborn difficulty).