Now that I've caught up with series 4, 5 and 6 of NCIS, I've gone back to the beginning of Tim's arc and these are the things I have noticed.
1. Tony is obsessed with Tim from the offset. When he goes to him in 'Eye Spy'? I flailed a little bit. He needs to track down a number, so the first person he goes to is a guy he's met once? And he's obsessed with Tim's alleged tattoo as well.
2. Tim gives as good as he gets from the start. This pleases me. Yeah, he's a lot more gullible, and calls Tony 'Sir', but he also sets Tony and Kate up to deal with Gibbs, which I like.
3. In ways I can't explain, that they deliberately set Tim up the way they did makes me so happy. It's clear they've always intended him to start off as a talented rookie who gradually becomes a badass, but also that they've always intended him and Tony to be buddy-cop-style friends. It appeals to many of my fictional preference kinks.
4. This has nothing to do with Tony and Tim, but Gibbs is way, way more lighthearted in these episodes than he becomes in, say, S4. You really only see that return to that level of bantering, grinny Gibbs in mid-S6, and by then, it feels hard won in an awesome kind of way.