Here's my opinion:
PVE - which class is in higher demand, and does better damage?
Sniper does better DPS...and it's ranged which means you can stay out of AOE damage that melee have to eat during some boss battles. Sniper also has a better rep as a DPS and would be more in demand.
FUN - Which class is funner, and has a more complex (not too complex!) rotation
I prefer Assassin here as far as 'fun factor' goes.
Levelling - which class is easier and funner to level?
I think Assassin (stealth makes solo'ing some Heroics possible). You can also avoid some trash mobs that you don't want/need to pull.
Storyline - Which class has a better storyline?
Sniper (IA story is my fave)
PVP - (not that important) which class plays better in warzones?
I like Assassin for PvP. You have lots of utility and can still do decent damage...stealthing around is also fun.
Companions - Which class has the best companions/storylines/romances? (advice on which companion to use while levelling is useful too)
I prefer the IA's companions for their character/storylines (don't know about romance...never done them).
Sniper: Kaliyo (tank) until Dr. Lokin (healer)
Assassin: Khem Val (tank) until Talos (healer). I tend to use Ashara just to kill mobs quickly though.
Both classes get their healers kind of late, which sucks.
So, it's a mixed bag for me.