A little "fridge logic":
1) How do the communication stones work again? Why did the stones from Rush (the stone Rush smuggled and the aliens stole/captured) and Young connect in the previous episode? I thought the stones were fixed to a particular other stone?
Pretty sure this is something of a ret-con. When the stones were first found, it was implied that they were linked completely to one other stone. I think Carter even mentioned that they might work on a quantum entanglement principle. Which would DEFINITELY make them linked only to one other stone.
If they work on some other principle, maybe the aliens were fiddling with the stones and managed to interfere with them? Yeah, this one is really shaky.
2) So the Aliens can burn holes into the Destiny and capture people, they can dock their shuttles. But they cannot get aboard? What's stopping them again?
Or can they actually get aboard, they just can't get control over any of the ship functions?
Cowardice? Or maybe it's as simple as not having a "Rosetta Stone" for Ancient language. Hieroglyphics were impenetrable until that stone was found, after all -- and all of those involved were *human* languages. For complete aliens, deciphering an alien language and script would probably be ridiculously difficult. Granted, I would assume they know it now, based on their capture of Rush.
Also, for all their technology, we've never seen one with a personal weapon. And it was pretty easy for Rush -- weakened from his time in a tube and operating purely on rage -- to overwhelm and strangle one of the aliens with his bare hands. And he's not even a trained combatant!
Besides, if I were those aliens, I'd be a bit worried about how many holes I punched in Destiny. Even if they can't read the script or understand the ship's systems, the hull scoring and visible age makes it clear that ship has been around a long, long time.
----------------------------
Let's look at it from a slightly different angle -- what's the downside to them at the moment? These aliens are aboard (that breathe the same atmosphere, even!) and fixing the thing up. If I was one of those aliens, I would have just hung back until the ship is working a little better and *then* invaded. If the aliens aboard aren't being threatened, they're not going to look for tracking devices and survival would be more of a priority than fixing up the weapons and shields...
Also, do they look like taller, blue Asgard to anyone else? They have that same spindly look to them and the shape of the head reminds me of Thor's race.