...the part where Rush came in the room, saw the dead guy, and removed the gun (to plant in Col. Young's quarters).

...who else thinks Rush shows up in that crashed alien ship after a couple episodes?

It incriminates him - Raises question as to why Rush didn't return. However, he could have truthfully said that he and Rush got into a fight and rush was knocked out. Understandably, he ran back to the stargate and still only made it with a few seconds to spare. There was no way that he could have carried Rush back and both of them make it in time. I would have understood the circumstances if I were on the ship.

I thought about him coming back in the ship. However I thought it more likely that he gets inside, does some repairs and makes a radio call to its alien owners. Another writer's possibility would be that the guy with "expanded chair knowledge" wakes and figures out how to turn the ship around and go back for Rush.

I was expecting humanoids like the Go'auld, but it looks quite shiny.

Who thinks the alien heads are a workover of the Crystal Skull in the last Indiana Jones movie? Oh and Mike, we both called it. Ship too damaged to fly - activated a location beacon while he was playing around with it.

They find another ship attached to the bottom of destiny and it has a tracking device in it (a ship they didn't know was there). But there is the one Rush and Chloe came back in. Why doesn't that one have a tracking device in it too? You could say they already jettisoned the Rush/Chloe escape ship except that there really is no feasible way to do it except from the alien ship itself. Will this other ship play a role later or just be forgotten? If I was Rush or Eli or any of the other scientists, I would be all over that thing trying to figure it out.

The one with the tracking device (supposedly) is detached forcefully. literally as the shuttle fires on it to do that. Therefore, if there was no other way do that without having someone in the shuttle (even a timed thing) then using the shuttle to do the job would be probable. And we know from what they said that the aliens were probably tracking the destiny for, well, a long time, and we did see that ship detaching at the end of Air Pt 3.

Rush keeps talking about how the aliens have been tracking the ship for a "long time, probably even before we arrived", but he also states - we have to assume correctly - that the aliens have never broken through the shields. If that's the case, an alien ship couldn't have attached itself to the hull, or they would have captured Destiny a long time before the team even arrived. So there has to be another tracking device, or another means for them to track it.

One thing I don't understand though, is the Borg-like mentality. They've been trying to get through the shield for a long time. They know that one ship alone can't break through the shields. Three ships couldn't do it either. So why not send an Armada if you want it that bad? And if you've been trying for that long, why have you suddenly increased your attacks if you know that the team - that Rush says is unimportant to them since they only want the ship - is now suddenly onboard?