You should try getting 3x P/P breed Nexus Whelplings. They are found in Coldarra in Borean Tundra. Get them to level 25 and make them Rare. Have them use the moveset: Frost Breath, Mana Surge, Arcane Storm. The three of them will end up punching through the defenses of most pet battles that don’t really require a specific strategy and some that do.
It’s also good to have a 2x Mechanical Pandaren Dragonlings for certain leveling strategies, but I forget the exact setup at the moment.
Aside from that, I almost always do not collect more than one of a pet. Mostly you’ll never encounter a need for doubles. There’s some rare breed pets you can find on the Auction House if you’re really tuned in to Pet Battles, but I can’t imagine this being that relevant to the average user.
If you want a fun hunt for a secret skin, try for the gold and silver variants of the Mountain Cottontail.