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I don't judge based on designs because I pretty much love all of them equally
However, judging by pokédex I go:
3 > 5 > 1 > 2 > 4 > 6
Hoenn's is diverse, has mostly new creatures with a few old buddies returning, and mirrors the tropical-ish island theme fantastically
Unova dex is very ~complete~ and has an amazing balance of types and designs (everything from weird to cute to cool) and does the whole "reboot" dex thing pretty good
Kanto is diverse and I guess just sets the standard, it doesn't stand out a lot but it doesn't have any problems, really
Johto has my favourite pokémon designs all around and compiements Kanto really well, the only problem I have is that some of the mons got locked into the postgame instead of doing like Hoenn
Sinnoh's dex tries to be all cool and hip but it lacks diversity (fire types getting the short end of the stick especially) also a lot of mons are trade evolutions and so it sucks if you have to play alone, platinum also locked skuntank, mismagius, honchkrow and purugly out of reach. Also I have a major complaint on things like Gliscor and Yanmega not getting Fly
Kalos is a huge clusterfucky dex that fails to highlight the new designs introduced, I get the idea but the execution was a huge mess. Also but not my main point: the new designs make use of having no more sprite limitations which makes them end up having lots of tiny details (believe me I've sprited barbaracle in the past and also thought of attempting xerneas but gave up)
