Does anyone have any ideas for what characters I should include?
Mega man>Mega man X>Mega man X (in X3 Upgrade armour)
Zero (X3 variant)>Zero (Zero series variant)>Black Zero
Kid Link (Eevee)>Adult Link (Jolt)
-------------------->Goron Tunic Link (Flare)
-------------------->Zora Tunic Link (Vape)
--------------------> Doppelgänger (Dark) Link (Umbre)
-------------------->Silver or Gold Tunic Link (espe)
Kid Zelda>Shiek>Adult Zelda
Haseo>Haseo (2nd Form)>Haseo (3rd Form)>Haseo (Xth Form)
Skeith>Skeith (Berserk)>Skeith (Xth Form)
Kite>Azure Kite
Orca>Azure Orca
Balmung>Azure Balmung
Ovan>Tri-Edge Ovan>Rebirth Ovan
I'll add more as I think of them.
Also I'd make Ronald non-evolving if you plan on including him (and the proportions on that sprite hurt to look at, no offence).
Also, What tool are you using to replace the sprites, I'd recommend "GBA Pokemon Game Editor" which is a multi-tool, and one of the tools allows you to edit the way pokemon evolve (it can be found at the pokecommunity forums).