1. Hoenn/Sinnoh
2. Kanto/Johto
4. Unova
1. Hard to decide, I love both, really. Basically I grew up with Hoenn, but I love Sinnoh too. I really liked the 4th generation and the games of it. It had an awesome atmosphere to me, something really deep. Also I really love the music from Pearl/Diamond/Platinum. As for Hoenn, it had amazing music too, atmosphere is something that I will never forget, and I love Pokemon from 3rd generation. I spend so much time playing games focused on Hoenn, that it really got stuck in my mind and I think... it beats Sinnoh and it is so far my favourite region ever. I hope they will make the remake of it, if yes, I am totally going to buy the game on the first day!
2. Another hard-to-decide. Some may think how I can not like Kanto, it is the first and all. Well... I hate some places in it and after beating the games with it 100 times it got really boring and basically when I see Kanto I want to puke. Also I didn't really like all the complications with going into millions of places just to get some items to progress through the story. It is not like that I love easy games or something, but... call me idiot or not, I still hate that tall tower in Saffron. The music in this region is average, nothing special to me, except few routes which are really nice. Some things about this region that I love, are for example glitch in the first versions (Missingno! I love it. ), atmosphere that sometimes appeals to me and well... there was a time I really liked that region.
As for Johto, I never really liked it and somehow I don't feel the bond with it. I always knew the maps for all regions from memory, in Johto somehow I was always feeling lost and never remembered what to do to progress through the story. It's just average. Music is average, everything is average and sometimes pretty boring. I don't really feel the atmosphere of that region. Also I didn't really love the pokemon from 2nd generation. Well, things I liked though are: Music from Violet/Olivine City (One of my favourite themes from Pokemon) and few other tracks, Pokeathlon introduced in HG/SS and that you can have 16 badges and the nice, challenging battle on the end.
3. Unova. Oh my, Unova. This is sadly just a fail region. It seems just too small and boring to me. And it's too modern. Everything is just... meh. I don't like it at all. Game gets boring as soon as you beat it. Who cares it has got cool graphics, it is missing that nice feeling in it. 5th generation Pokemon aren't that great again, maybe few of them seem okay, the rest is just weird or not-pokemon-alike. But one thing I really, really, really love about this region is... music and epic story. Yes, it got awesome plot and awesome music filled with epicness. Can't describe how amazing I felt listening to credits music. Wow.
Plus one thing, N is the first ever character from Pokemon that I really like.