Oh fine, I'm at work so no better time for this than now…
Well , at first he wore those sneakers, at least in the pilot and in most of the first season too, the black ones with white tips. The whole style of the show was different then for all the characters, more down to earth colors, plaid, normal clothes. Like we've said a million times before, they were trying to adabt with the rest of the people. So his style and shoes were normal. But also the style in pilot was still 1997ish and maybe continued with that in the first episodes.
The first time we saw the black combat boots was in
Heavy Metal, which was a very rebellious episode for him, so the shoes perhaps reflected on his actions too. He still went back to sneakers though in
The Queen's gambit and they didn't resurface again until
Vick's chip. This again was about him going against Derek and Sarah at some things. But then the sneakers came back again in What he beheld and obviously he still wore them in S&D. But after that it was all combat boots all the time starting from episode 2. Until he got those new boots in
Ourselves alone, which is also the episode when he started to change for the better and his shoes reflected on this change too.
I like the combat boots look more myself, though the sneakers are better for escaping terminators out to get him than boots that were often not laced completely. He should have tripped over more often if you ask me, it would have made for a good comic relief, messiah's can be clumsy too!
So there you have it. I deepened the analysis for you guys! Feel free to point out any mistakes.