I know you progress through zones and it affects who you fight for in Cyrodiil and the Imperial City, but is there a certain alliance which is better to join for PVP, or is it balanced?
It may depend on your pvp goals as well as your platform/server. What are you looking for in pvp? Largest population? Best small scale? Easy pug groups? Give a bit of details on what you'd like to get out of pvp and you may find some good suggestions on the best alliance for those goals.
I know you progress through zones and it affects who you fight for in Cyrodiil and the Imperial City, but is there a certain alliance which is better to join for PVP, or is it balanced?
If the populations for all the factions were all the same or there was some mechanism to cap all at the lowest at any given time, it would be balanced. But as it is, the faction wiht the greater population on average (if it is a significant enough difference) during the campaign almost always wins.
AD has castles, DC has forts, EP has keeps. Each alliance has one flagged town inside their home territory, blues and reds have an unflagged town. AD has the only ocean fishing hole. The Allessia bridge is almost always a hotspot, closer to AD home than to EP home. Very rarely is there action in the wilds of the snow covered land.