I'd say Generation 5 is the best generation *in isolation*, fitting its status as a soft reboot that ignored some "sacred cows". Sure, people mock Trubbish and Vanillite, but the Gen 1 designs are more iconic simply because of time, they are *vastly* more blunt and unimaginative. Making a garbage bag look like a convincing living thing takes a lot more work than slapping a face on an indistinct pile of toxic waste!
Gen 5 doesn't take the premise *completely* for granted, Team Plasma puts the ethical question of it in your face and this stretch of the franchise gives you the counter-argument. The world is broadly and obviously non-static, in both environmental capacities and in having a soon-after sequel showing the world changing.
In other words, I prefer Gen 5 because it's basically the most "alive" of the series, with the "brain drain" kiddifying and "powerhouse" gimmicks kicking in right after with Generation 6.
But in terms of an exact single game, Crystal's a good option. The technical derps of building all the systems are mostly solved so the game's stable, it makes decent references to the first game without actually shackling itself to references like the B&W sequels, and it's very far up there for distinct content that doesn't go mini-game.
And, of course, it bypasses the trade-enforcing versioning arguments. HG/SS have this issue, as well as the gen 4 engine problems. Beyond those, it's personal preference around graphics, the other-gen 'Mons, and how they're supplied.
