Hmm. Well, let's see...
Kanto: currently, despite not being an OS fan, I prefer to to RGBY, simply because in Gen 1 the game was slow, tedious, mostly broken and not as engaging as other Pokemon games for me. However, I've yet to play FRLG to see if my opinion of Kanto changes, so this is not definite.
Johto: definitely the games. I really enjoyed Johto in HGSS (yet to play Gen 2) because even without Kanto, Johto is still a vast region filled with many interesting places and people. In HGSS, almost every city has its own character - Ecruteak City instantly comes to mind - and the characters within such as Eusine, Silver and Clare are really distinctive and enjoyable. Meanwhile in the anime, the region was still very vast, but the town's and cities definitely felt less unique and separate from each other. The characters were also still interesting, but a couple could've been better (aka Eusine, they butchered his character in the main series). Also, I do have to say that one of Johto's main appeals was the legend of the three beasts, and since that got a decent amount less focus I got kinda sad there, but that might just be personal.
Hoenn: I haven't actually watched much of Hoenn, but I'd probably still prefer the games from what I do know. I mean, the moment I realised one of the Hoenn champions was a CotD until Kalos and the other didn't even appear until Sinnoh my opinion was kinda brought down of the series. Also the Magma/Aqua arc sounds very inferior to the games, both in RSE and ORAS.
Sinnoh: games still. Now, I do have to say this one was at least a little closer, but only because of Riley. I'm definitely not a fan of Paul, for a start. While I do love Brock, he also felt like he had overstayed his welcome by then. Dawn is pretty cool - probably my favourite Pokegirl - but she's not exactly amazing. I also felt that the anime didn't have a solid conclusion with its villain arc, while the games (at least in Platinum) showed us what exactly was beyond that portal Cyrus went into, which actually felt more appropriate. Also Cynthia appears way too damn much I prefer the game since Platinum has this really vast feel to it, and Barry works fine as a single rival. The plot also had an at least somewhat solid conclusion. Also Cynthia appears less
Unova: Really?
Game - plot had me stunned, graphics are extremely pleasing to look at, villain arcs were satisfactory, rivals were worth remembering, both Reshiram and Zekrom got simolar amounts of screentime, so on and so on.
Anime - somewhat ok plot bug nothing like the game, graphics are eeehhhhhh, villain arc was ok but nothing new or worth my time, I keep forgetting the rival's names (Snivy boy and the one with the red shirt), Reshiram was heavily favoured, etc etc. Also we didn't need more FRRAKIN CYNTHIA SHOVED DOWN OUR THROATS At least the anime had Vic Mignogna?
Kalos: Aha! Here we go. While I loved Pokemon X to pieces for its music, graphics and new features, and while the plot was really good, they could've executed the villain arc a lot better. Along wanders Anime!Flare, and boy I love it. Yeah, sure, Lysandre has less personality, but look at the scale of the arc, the graphics, the inclusion of so many side characters that make sense to be there, STEVEN, it all works out so well.and while there are so, so many things that I dislike about XY and XYZ, I can't find myself calling it worse than the games at all, for three factors alone - the Mega Special, the Flare Arc, and the overall graphics of the series.