I have yet to try the 3 way PvP here in FFXIV but I think it's something that will more than likely stick. In other games with 3 way faction warfare there will always be a time where 1 side feels (and very well may be) it is getting the shaft by the other two.

Examples of games I myself played in recent memory being Planetside 1/2 and also The Secret World had heavy emphasis on 3 way battles. Honestly though even if it were just 2 sides here in FFXIV you would still have a bunch of bandwagon players jumping over to the winning faction. In 3 way battles the powerhouse has a chance of bullying too much and having the other 2 sides team up for their demise.

When players take actual strategy into consideration and not just trying to be on the easy win side opens up opportunities for awesome interplay between them. Takes players though. Not something SE can just fix.