My favourite region is a bit of tie between Kanto and Johto. For the longest time Johto has been my favourite, given that Silver was the individual Pokemon game that I've spent the most time on ever. Lots of my time went into playing that, training my favourites, searching for legendaries (although Hoenn was better in that aspect), and generally just having fun with it. It was also Silver that was the first game of my own, while Blue was shared between my brother and I. But I've definitely had the best memories and experiences in my Silver. Johto also introduced some of my now favourite Pokemon, main one being Lugia, which is my favourite legendary, for various reasons. I just feel like the second generation Pokemon are quite unique, and that was when the Pokemon designs were at its peak. All the ideas may not have been all too creative, but that can be applied to just about every region, but when I look at those, I feel like I'm actually seeing Pokemon, I just feel like that went downhill from the third generation. But yeah, loads of reasons why I'd like Johto the best.
Though Silver may have been the game I've spent the most time on, Kanto is the generation I've spent the most time in. My overall playtime in both Blue and Leaf Green is pretty long, and when you add the time spent in Kanto in the second generation games to it, it's pretty certain. And Kanto was the beginning of my Pokemon journey after all. I may have been a little kid at the time, but it still has an impact on me. It's where most of the nostalgia was whenever I'd left Pokemon for a while, and is usually the generation I'd return to, and even though the games featuring the Kanto region are growing pretty old, I still feel them as new and fresh. They may not have all the new mechanics, wild double battles and all that, but as opposed to a lot of the newer games, I never feel like I'm bored when I play them. And that's a pretty big factor when it comes to deciding these kind of things for me, so also the biggest reason why it lies at the top with Johto. Like with Johto, I also really like the Pokemon from the first generation compared to the newer ones, and you can't really say that they don't feel like actual Pokemon, considering they were the first lol.
But yeah, I don't think I can decide between the two, as they've both meant a lot to me, and I pretty much love them both, but if I really had to choose one, I think I may be leaning a little bit more towards Johto :/