All shiny legends certainly may throw some people off, unless given a choice.
But mmm, it's been so long since I last played an actual rom hack. The Gold and Silver FR/ LG remakes were pretty nice, as well as the game enchanting/ trade evolution removal/ all pokemon available in-game hacks of the DS gen.
As far as I remember from rom hacking, the possibilities were rather limited compared to those of Pokemon Essentials fangames though.
Speaking of which, I have quite a few of those lying around, and personally I enjoyed them far more than simple rom hacks.
For the game to shine through the rest as a rom hack, quite a lot would have to be done. I'd rather recommend considering Essentials, as I've seen people do similar things in their fangames to what you wish to go for. Like Godra for example, two starting towns based on choices, possible career choices, starter pokemon determined by a little "test", and as far as I remember, advancing didn't require you being stuck in one tiny area 'till a gym is beaten, but I might be wrong on that one.
One of the fangames even offered to play pre-made challenger modes like Nuzlocke, etc, if the player wishes so, and that was a really nice little add-on.
All in all, being a script package to RPG maker, it in general offers more possibilities to branch out for a truly unique pokemon fangame.