From a pvp point of view...

Arena PvP vs. Battlegrounds vs. World PvP.



With three in Arena, assuming an optimal configuration...
Your team will likely cap at a higher rating than going with five.
Three, like five, is a full group for a given bracket (3's vs 5's).



Battlegrounds...
You'll have a lot less blow them up, ability compared to a 4-boxer or a 5-boxer (who is often a 4-box + heals).
So, I'd imagine significantly less power in the larger scale BG's, or BG's with only a single objective at a time.
However, being 3 of 10 players (Warsong Gulch or Battle of Gilneas) instead of 5 of 10 players... should be a significantly higher chance of victory.



World PvP...
Your gank resistance while leveling, will be far more than a solo player, but not nearly the deterrent of a five-box.
Your ability to gank solos will be there, either way.
Your ability to hold their auction house or flight master (or whatever) in a opposing city, will be massively reduced.