Your best defense (as Advent) against bomber spam is the Halcyon Carrier's telekinetic push. This will break up that cloud of bombers and give your fighters time to destroy them. If you have three or four (plus sufficient anti-matter upgrades) you become virtually impervious to strike craft.
TEC can use their Kol with flak barrage or their Dunov with magnetism (flak barrage will require at least two Kol's synchronizing their barrages to ensure a kill). Vasari can use jam weapons to disable those bombers for a while. However, I personally think Advent is in the best position with telekinetic push and lots of fighters to back it up.
In any case, you should try to scout ahead of time to get an idea of what your opponent is doing. Mass bombers is a very devastating strategy, but if you attack before he has a critical mass of them you can clean them up quite nicely with fighters.
