Rares weren't ever supposed to be easy to get, hence the name. The old t50 was too easy, which is why it was changed to the arena system. It is possible to win rares from many of the AI decks; AI3 has some of the rares, halfbloods can in theory have any rare except the shards, although that's unreliable, and FGs have most of the nonshard rares, if not all. You can also win rares in pvp or from the arena. (rare spins at the end, or even regular spins if the deck had them)
What's the best way to get rares? I'd think playing against bronze league, or for certain ones, FGs. You can get arctic octopus and eagle's eye from Neptune fairly easily, and there's Miracles in a lot of FG decks, for example, and there's other rares spread out amongst the FGs. I think they're all actually out there somewhere, but some like Miracle or Eagle's Eye are far more common than one like Titan, which I think only Akebono has. (at least there's got to be some reason why I have 5 or 6 of every non-new shard upped rare except for titan, which I have 1 of :p)