As long as the custom moves are within reason (so let's NOT say 'Mewtwo used BrainBurster' or something dumb along those lines).
I think it wouldn't hurt the authenticity (rather, the authentic feel) of the hack to include custom moves. I gather you're including at least some, if not all of the later-generation Pokemon, and so I think having some new moves would just benefit the hack.
I'll also say that you should be wary of overthinking things like that- remember, you are one person, working on a hack of an existing game, you are not a professional. By all means, aim high, as you've done all along, but just be wary of getting bogged down by things like 'Will this look professional/authentic enough?'. But back to what you asked:
I do not think that adding new/custom moves to the game would make it feel less authentic.
The end. :P