It's easy to take out the waves of 1000+ ships if they just run around in small groups and keep raiding resources, but if they stay grouped and go straight for command stations, you're pretty much screwed.
Obviously force fields will defend the command station, but they do nothing against infiltrators, and not much to bombers.
The most difficult thing is that by the time i finish off a wave, often, another one appears within a few minutes. I never have enough time to actually attack a planet as you are constantly fighting to keep your planets clear of enemies.(when i did attack, a wave would come at an inopportune time and i wouldn't have enough time to fly my fleet back, or even scrap my fleet and rebuild it at the attacked planet) Of course you can always just set a bunch of ships on FRD mode and hope for the best, but against faster ships, they almost never encounter the enemy.
If the game could be won by just defending, the wave size would probably be fine, but since you have to attack into the heart of the enemy forces and take out their home planets...
If waves happened less frequently, like once an hour, and we had say 5-10 minutes warning before the waves arrive then this wave strength might be feasible. As it is right now, we would often get only 2 minutes to prepare, which usually involves building as many counter-ships at that planet as possible and building turrets to cap at that wormhole.