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Red/Blue were solid all around. Red is easily the most gorgeous game on the GBA. Plot is decent. Balance was also decent - it was a simpler time with fewer move possibilities and less bullshit, so the balance was pretty fair.
Time/Darkness is the same as Red and Blue but highly refined in almost every way. Plot is better, characters are better, art is better, music is better, gameplay is better. And the game is long as fuck, too - when the credits roll, you're only like half done. There are lategame and postgame moments where the game will just shit on you, though. Some say they're two of the best Pokemon game ever made, let alone just PMD games.
Sky is exactly same as Time/Darkness but with some extra plot padding. If you were considering Time/Darkness you might as well pick this one up instead.
We don't talk about the shitty Japan-only Wiiware shit.
Gates feels unfinished. It reeks of experimentalism where the devs were clearly trying to shift the game into 3D and making it more casual accessible and built for short play. Characters and gameplay are pretty weak, but the plot is actually really solid. It's basically what X and Y were to the main series - fresh, flashy, 3D, but super unpolished.
Super is the polished answer to Gates. They perfected the gameplay, making it much more rapid and challenging while still being fun. Characters are good again, plot is still pretty great.
If you can't play them all play Super and Sky/Time/Darkness. Red is really easy to emulate if you don't want to buy it. Gates isn't great but it's not bad. The order you play them doesn't really matter, though Super does make nods to the ones that came before that you won't catch if you play it first.
