Well to be completely fair, it shouldn't come as a surprise to anyone. Before wolves den even came out they talked about Grand Company vs Grand Company vs Grand Company combat, which was a big clue that the one your in matters, and the pvp system itself shows it matters which one your in. I cant see a ton of people being surprised by this if they even read patch notes and never look on forums, it was all spelled out months ago. Arena pvp has generally always worked where its teams, so the fact you can work with other GC people makes sense there.

Now is it a good idea? I dont know, they probably could have just done 3 teams or took a page from guild wars and did server vs server vs server but the fact there are 3 GC's in the game and 3 sided pvp just kinda makes sense.

Maybe they will make it so your rank carries over if you change if enough people want it. Its not really a big deal to swap them PVE wise, so that might all work out ok.