I do agree that the "Golly gee brilliant whiz kid" angle was a bit trite. "The Last Starfighter", take II. And I didn't like how much they milked it in the beginning. But then, they backed off enough that it became easier to tolerate Eli.
Definitely, the "bad guys" were very one dimensional. At first. When some of them got to join the crew, that opened up things a bit. I don't recall the guy's name, but the one who got the most time was a pretty likable/relate-able character.
I don't think the 1st season was quite so bad. They kind of captured what people would feel like in such a situation. The complete disorientation of being on an alien ship, faced with immediate challenges that you aren't quite sure how to fix. By the 2nd half of the 1st season, I felt the series was starting to improve, and then got reasonably good in season 2. ALL sci-fi series face great challenges in the first couple of seasons, as writers figure out what works and what doesn't and actors find their footing. I actually think SG-U did better than Atlantis in this regard. It took a while longer for SG-A to get going. In the beginning, it felt so much like a "lesser" SG-1.
The ending was not lame, IMHO. Eli is a genius. He has some kind of savant quality about him, that even he didn't quite realize until his involvement with the Stargate command. He still felt so inadequate for quite a long while. It wasn't until towards the end of season 2 that he started to acknowledge his gift... that he really has the stuff. Dr. Rush confirmed that as well in conversations with Colonel Young.
Anyway, the thing is... we really don't quite know if Eli DOES know how to fix the chamber. That's what's so great about the ending. There's this uncertainty... did he really believe he could do it, or... did he sacrifice himself so that no one else would have to?