I depends what you want to use them for. Overall, Vaporeon has a higher base stat (525 as opposed to Jellicent's 480). It has higher HP and sp. atk as well, while Jellicent has higher def. and sp. def.
If you wanted type coverage, I would go for Jellicent. If you wanted a Pokemon with some bulk and could turn out more special damage, I would go for Vaporeon. Jellicent also has a larger movepool (most Eeveelutions have pretty restricted choice of movesets), and it has Recover. That move made Marlon's Jellicent seriously annoying...
You have to remember that Jellicent(s?) are easier to obtain, as Eevees only appear in Castelia City Park (5% encounter rate), whereas Frillish/ Jellicent appear quite frequently around Undella Bay and Humilau City, though you could only get it later in the game.
Also, as this is an in game team, I would recommend Water Absorb for both Jellicent or Vaporeon. Hydration for Vaporeon is best used on a rain team, and Cursed Body has a 30% chance of activating, which isn't that helpful. Damp is more or less useless, since Self-Destruct/ Explosion won't hit Jellicent anyway because of its Ghost typing.
Last point: I would consider Gothitelle (Black 2)/ Reuniclus (White 2), since imo Beheeyem is a bit too frail. I've used it before, and its too slow to get many chances to attack before it's KO'd (unless it has Trick Room), whereas the other two Psychic types have a bit more bulk, but that's just me. Though, Gothitelle doesn't have really useful abilities, so maybe Beheeyem is better for a Black 2 game.