Even though this was answered a long time ago, I'm going to give a slightly different take on the answer with some additional information from a short time playing as both. I won't go into the perks of both since that has already been done.
NB: This answer relates to Dawnguard although the original question pre-dates the Dawnguard expansion. However, since many people, like myself, may think the original question is about DG, I will leave this answer here with the permission of the moderators.
- Quest differences and location:
From the point of view of quests, if you compare the quests for both factions you'll see that the locations don't have much difference to them. The first quest for each faction is different, but after that they're largely the same apart from the fact that you're either playing Dawnguard vs Vampire or vice versa. The current Wikipedia Dawnguard article mentions this, saying:
if the player character refuses Harkon's offer [of becoming a vampire]
and returns to the Dawnguard, the plot plays out nearly identically,
albeit viewed from the perspective of the Dawnguard.
Obviously, you will not have access to Castle Volkihar if you choose Dawnguard or Fort Dawnguard if you choose the vampire side. Functionality-wise, the Fort is much more focused on weaponry and has a blacksmith, general goods merchant, arcane enchanter and forge. The Castle is more magic-orientated and has access to the Bloodstone Chalice, Amulets of Night Power, and Rings of Blood Magic. Looks-wise they both have a Gothic feel to them, though the Fort is more classical-Gothic and the Castle is more horror-Gothic: their locations match this since the Fort is in the auburn leafy clearing of Dayspring Canyon near Riften, whereas the Castle is the inhospitable cold of the sea west of Solitude.
- Daylight exposure and travelling
As a vampire you do have to be careful when out in the sun. I play as a Redguard and like to explore Skyrim at all times of the day and night, and being out in the sun can damage your health [this does not apply to houses/caves/dungeons though]. If you like to fast travel this can cause problems, with sun damage or death being the result. Additionally you can get attacked even by your own brethren if they discover you're a vampire pre level 4 - I was killed by my own housecarl after he discovered. If you're level 4 you will get attacked by NPCs, pretty much everyone hates you.
Something else which hasn't been mentioned is any alterations you want to make to your character appearance. I'm the kind of person who likes to make occasional small changes to my character's appearance [hair/warpaint] via Galathil in Riften. When you become a vampire you get glowing red eyes all the time, and I felt that these didn't go well with my look, so I wanted to make changes to my character's physical appearance to match them. However, if you go to Galathil after becoming a vampire she will say she cannot make changes on the undead. Even the 'showracemenu' console hack will not work. Additionally, your appearance will become more haggard the longer you don't feed. If you're the kind of person who cares about your character's look, these things can bug the hell out of you.
It also comes down to whether you want to play weapon-based as part of a faction for the better of Skyrim, or magic-based for the betterment of your own personal cause, and how well these tie in with the kind of character you're playing [though you can mix and match, of course] and what they would do.
Choosing Dawnguard is not the end of your potential as a vampire. You get the opportunity to become a vampire again in the Chasing Echoes quest, you can also switch between vampirism/lycanthropy if you ask Aela when the questline is over. You can still become a vampire Lord after completing the main questline by asking Serana to turn you, as long as you have not cured her of vampirism first. Either way, you will still get endless radiant quests for either side.