The only difference is that Genesect might be able to take a hit from a priority attack or actually do something when U-turn isn't the best option against the opponent. Also, it can't deal with rocks, while Genesect can, to an extent.
Also, 252 attack scarf does more damage, if barely.
252+ Atk Choice Band Ninjask U-turn vs. 252 HP / 0 Def Heatran: 34-41 (8.8 - 10.6%)
+1 252 Atk Genesect U-turn vs. 252 HP / 0 Def Heatran: 38-45 (9.8 - 11.6%)
Assuming download boost, which is not always the case (I kind of dislike how this forum treats download as a free choice band/specs with no drawbacks, it's not parental bond folks).
Also, Ninjask can take a mach punch surprisingly well, but anything else (except maybe an unstabbed, unboosted base 40) and it's boned.
Agreed with SR, I'd be a fool to argue with that, though it's immune to every other entry hazard for what it's worth.
Banded Night Slash is surprisingly effective against subbed ghosts though, and AAce can net the occasional surprise KO on a grass, bug or fighting type, especially trenevant, breloom and gourgeist, but otherwise agreed with that gene is overall more effective in his non u-turn options, especially special scarf (not entirely convinced that phys scarf gene has better coverage then ninjask, but he does have harder hitting moves and the ability to run special moves anyway).
Once either of them are locked into a move though, checking them is almost trivial because of the problem that plagues all choice users, so you better have a KO to show for it or else bye bye momentum.
Anyway, the point of all this is not really to try and argue Ninjask > Genesect (because that's blatantly false, and we all know it), it's to say that 1. if all you want to do with a Genesect is spam fast u-turns all day, here's an NU buddy that is almost just as good at that and 2. That there are obviously other aspects to Genesect's power besides u-turn.
If only he got knock off... Oh well.