Pikachu: movepool changes (1 single move); inability to evolve (can't use Eviolite);
tiered together
Pichu-Spiky: unobtainable in Gen 6, just design changes;
if it was legal, I guess it would be tiered together with regular Pichu
Unown: design changes (why I can't choose any letter but A on PS? x_X);
tiered together (there aren't alt forms on sim)
Castform: type changes; only in-battle form; (extremely) volutile;
tiered together (and it's pretty obvious, since you can't decide only by yourself what Castform alt form you will use and your opponent could trigger other forms in any moment of the battle)
Deoxys: stats changes; movepool changes;
tiered separately
Burmy: design changes;
tiered together
Wormadam: type changes; stats changes; movepool changes;
tiered separately
Cherrim: design changes; only in-battle form; volutile;
tiered together (every Cherrim can potentially be Cherrim-Sunshine unless you ban Sunny Day/Drought/Desolate Land from everything)
Shellos/Gastrodon: design changes;
tiered together
Rotom: type changes; stats changes; movepool changes (1 single move);
tiered separately (it's important to note that Rotom-forms were tiered separately even when they shared the same type as Regular Rotom: however, they were tiered both as Rotom-A and Rotom-Wash/Heat/whatever);
Giratina: stats changes; ability changes;
tiered separately
Shaymin: type changes; stats changes; ability changes;
tiered separately
Arceus: type changes; move-typing changes;
tiered separately
Basculin: ability changes:
tiered together
Darmanitan-Zen: type changes; stats changes; only in-battle form; revertible;
tiered together
Deerling/Sawsbuck: design changes:
tiered together
Kamis (Tornadus/Thundurus/Landorus): stats changes; ability changes;
tiered separately
Kyurem: stats changes; ability changes; movepool changes (2 moves);
tiered separately
Keldeo: design changes;
tiered together (only other notable difference is that Regular Keldeo can choose to not bring Secret Sword while Resolute can't).
Meloetta: type changes; stats changes; only in-battle form; revertible;
tiered together
Genesect: move-typing changes;
tiered together
Vivillon: design changes;
tiered together
Flabebè/Floette/Florges: design changes;
tiered together
Floette (AZ): stats changes; movepool changes (1 move); inability to evolve (can't use Eviolite);
tiered separately (if it was legal)
Furfrou: design changes;
tiered together
Meowstic: ability changes; movepool changes;
tiered together
Aegislash: stats changes; only in-battle form; (extremely) volutile;
tiered together
Pumpkaboo/Gourgeist: stats changes;
tiered separately
Hoopa: type changes; stats changes; movepool "changes" (regular Hoopa can't successfully use Hyperspace Fury);
tiered separately
All Megas: (some) type changes; stats changes; (some) ability changes; only in-battle form; irreversible;
tiered separately