I never really liked the addition of the wormhole aliens. They're a never ending threat that you can't fight back against - all you can do is kill the ships that come through.
Now if there was a way to research their engine tech and learn how to travel the wormholes, then send fleets back through after them - then it wouldn't be so bad. At least then you would have a goal - stop their incursion once and for all, even if it takes 500 years of building up to do so. As-is, there really isn't a goal associated with the wormhole aliens, other than kill them as they come through and don't die. I mean, at least give us a way to close up their wormholes.
It could have been done really well, like being able to research the tech that opens the wormholes and discover how to close them. Say for example to close them you have to destroy the wormhole generator on the other side, which involves sending a fleet through to take out their defenses and destroy it. The catch is, once it's gone the ships left over there have no way of getting back - so you're left with a choice of how many ships should you leave on the other side to destroy it, and can you get away with leaving one small ship to finish it off when they might get reinforced at any time. Maybe you could eventually research the wormhole generators themselves, and build your own to be able to launch attacks against their generators and get your ships back home with your own generator, then turn it off until you need it again. Eventually you may even be able to turn the tables and get on the offensive, making strikes against their worlds, which would be extremely well defended and require a massive strike force to even have a chance.
Just an example of something that IMO would have made for better gameplay than "Wormehole opens. Aliens stream through endlessly."