OK, firstly, the puppets and special effects in general look ridiculously better in the third and fourth seasons, and the second has a firmer grip on things, too. But really, I think you'll be quite pleasantly surprised with the overall production value of the series going into its second half. There's a big leap between years two and three, and for the life of me I've never gotten around to asking anyone why. The show was never exactly a breakaway hit ratings-wise, so I dunno.
As for the theme song, it's so ingrained into me that I can't imagine disliking it, but I have a long history with the show! That said, I'll spoil for you that the theme song changes in the third year (there we go with big alterations again) and Crichton's narration changes every year, too, which is neat. Anyway, point is, I think the second theme is loads better, and sounds much crisper and higher-quality to boot.
If you liked "I, ET", I think you're in for a real treat with the show. Many consider that a pretty bad ep overall, and a really weak one to show as the second hour of the series, and I agree with them. But I do think it has some saving graces. Aeryn and D'Argo in a tree (thankfully, not K-I-S-S-I-N-G?) was great stuff in particular, I thought.
"Exodus from Genesis" is really good for the first half of the first season, which is certainly the weakest run in the show. (Which is always nice, because it means brighter pastures are ahead of ya!) The space bugs are actually kinda cool, and seeing someone so down-to-Earth (except not...) as Crichton handling sci-fi tropes is really fun.
"Throne For A Loss" is also solid stuff for its era. Rygel comes into his own in this ep, although I think the writers still struggled with him a little for several more episodes. Many would disagree with me, and I respect that -- I think they wrote him well for what he's presented as, but he's just not all that deep, yet. Yes, believe it or not, even Rygel gets deep!
As for B5, I guess you didn't miss too much without "The Gathering", and seeing all the cast changes is kinda odd, anyway. I'll try to remember to point something nifty out about a certain character's arrival on the station later on, though, as she'll in fact be familiar to all those who watched the pilot!