Been playing since beta, more or less, and here's my observations:
-Population doesnt really change between the alliances. It seems like most, if not all, players have characters in more than just one alliance (I've got a character in all 3, and most of my friends/guild members do as well) - so that kinda balances the populations out.
-PvP does have some population imbalances, but it's based on which pvp campaign you choose (pvp campaigns are like seperate servers you join when going into cyrodiil). Some campaigns have a lot dominion, some have a lot of covenant, some have a lot of pact, but you can pick which campaign you want to join when you first enter cyrodiil so that isnt a big issue.
As far as flavor goes, and I'm more than likely a little biased here:
-The Aldmeri Dominion has the most beautiful zones and the most interesting quests. Everything is vibrant, there's a lot of deep lore to be explored, the NPC's are all very well written and voice acted, you really get drawn into the quests and decisions. The only zone in the AD that I didnt feel this draw to was Malabal Tor, the quests there were a little on the slow and boring side and I was overlevelled for the place by the time I got to it, so I rushed through and on to reaper's march.
-The Daggerfall Covenant has the second best quests and zones. The zones are not as vibrant or pretty as the dominion zones are, but they have their own charm. Rivenspire and the Alikir desert are both pretty awesome. The NPC's are decent, rivenspire was particularly interesting in my opinion. Bangkorai was a bit on the boring side, but it does have it's share of fun quests where you're doing important things.
-The Ebonheart Pact, In my opinion, is the worst of the three. I havent gotten through all of the zones on that one yet, but the first four have all been terrible. Everything in the pact is drab and dull, it's like they desaturate your graphics everywhere you go. The NPCs are not particularly interesting (some are, but they're very few in number), the voice acting doesnt seem nearly as good as it is for the covenant or dominion, a lot of the NPC's are just downright unlikable, and the quests dont have that spark to them that they need in order to draw you in and be genuinely interesting.
My pact character has gotten the least amount of play simply because I cant bring myself to trudge through the boring zones and uninspired quests they've got. I highly recommend the dominion, but if you're more a fan of the covenant's theme and style it's a very good option as well. Dont go pact unless you're extremely drawn to one of their races, however (because that's the only thing that will keep you playing there).