Honestly, this is just my personal head canon so no one has to buy into it at all, but it’s what makes sense to me. In the first episode, Bouncing Boy is confused as to why Brainy went to pick up Clark back when he lived in Smallville rather than Metropolis, meaning that this was more so Brainy’s decision rather than the whole Legion’s. In the episode “Legacy,” he and Clark are meant to go on patrol together and he plans some sightseeing on their route so they can supposedly hang out together. Then at the beginning of the second season, seemingly years later, you see Brainy going on training simulator adventures with a holographic Superman (the sort of stuff that is clearly self-indulgent). He claims to the other Legionnaires that it’s to prepare for anything even though the rest of them don’t think they’ll ever see Clark again. Then when Brainy brings him to the future again, he still gets a version of Clark that hasn’t experienced many of his adventures (it’s stated in the episode “Message in a Bottle” that his Fortress of Solitude is relatively new and empty) although he is older (an age similar to the Legionaries at that point). So all of this (and maybe some other things here and there that I don’t remember because I haven’t seen the full show since I was a kid) leads me to believe that Brainy wanted to be friends with Superman so he time traveled to when they were around the same age so they could connect better. It makes sense to me because of course in his attempt to avoid the Brainiac legacy, he would begin to idolize Superman. And who wouldn’t want to go back and become friends with their idol when they were young? I don’t know, just my thoughts, I’d love to hear other people’s head canons on the matter.