In the later seasons they always mentioned that Cory & Topanga have been a couple since they were 2+ years old, but in the earlier episodes Cory always made fun of her and didn't like her.

For continuity purposes, ignore the first season. That was more of an experiment than anything. Topanga wasn't even in his class all year.

If you don't want to ignore the first season, then think of it like this...

Cory and Topanga were close as young kids. As they got older, Cory developed his "I hate girls" phase and Topanga turned weird which caused a rift in their relationship, even though there was some sparks in several first season episodes.

yeah BMW isn't known for it's continuity. They've even made inside jokes about it on the show.

I guess what happened is in the later seasons they got all new writers who changed the history of Cory and Topanga :)

Cory: Mom, Listen, I haven't been together with Topanga for twenty-two years, but we *have* been together for sixteen. 'Kay, that's a lot longer than most couples have been together. I mean, when we were born, you told me that we used to take walks in our strollers together in the park. When we were two, we were best friends, I mean, I, I knew everything about this girl. I knew her favorite color. I knew her favorite food. Then we became six, you know, and Eric made fun of me because it wasn't cool to have a best friend that was a girl or even know a girl, so for the next seven years I threw dirt at her. I like to call those "the lost years." Then when I was thirteen, Mom, she put me up against my locker and she kissed me. I mean, she gave me my first kiss. She taught me how to dance. She was always talking about these crazy things and I never understood a word she said. All I understood was that she was the girl I sat up every night thinking about, and when I'm with her I feel happy to be alive. Like I can do anything. Even talk to you like this. So that's, that's what I feel is love, Mom... When I'm better because she's here... and now she won't be. So we're finished.