I personally played Alliance since Beta, and then up to about 4-5 months before Wrath hit I took up Horde (So I could RAF level some Shamans to see if it would work cause alliance you can't). As of probably last month I ended up pretty much ignoring my Horde Toons (4 X Shaman, 1 DK, 1 Pally all 80) because the horde on my server and battlegroup are terrible at PVP. Most of my alliance friends are still around so I decided to play with them again.

I guess it really depends on what you want to accomplish in the game and how well each faction is on your server compared to the others.