I haven't been back here in a while and stopped playing Skyrim for a while as I really got into BF3. I recently got back into Skyrim to finish Dawnguard and enjoy Hearthfire and Dragonborn. What I was wondering is what are the ramifications when I chose the vampires. I had heard they run rampant all over Tamriel running through every town causing trouble. Is this true? I just completed the blood chalice, should I go further?

Well I don't think you could change factions after that encounter with Harkon, in fact if you chose the Dawnguard there is an even greater chance of vampire attacks happening since they now hunt you down too.