First the most part right on, although I would argue that "overlooked" can qualify as "underrated" by itself. If people aren't buying it, that says that there is a poor or at least indifferent opinion of it by the general public. Whether that opinion is educated or not is a different issue.
- Actraiser
I don't think ActRaiser is underrated, or at least not the first one. But hell, they're both awesome anyway.
So, besides that, here's some others that come to mind:
-MegaMan X6 (PS1)
-MegaMan Xtreme2 (GBC)
-MegaMan X Command Mission (GCN)
-Pretty much the entire Legends and ZX series
-Godzilla: Monster of Monsters (NES)
-Godzilla Unleashed (Wii)
-Joe & Mac (SNES)
-Shadow The Hedgehog (GCN; it's no SA2, but it's better than most give it credit for)
-Sonic Adventure 2 (DC; less by the general public and more by the so-called "professional" press)
-Mario Kart Double Dash (GCN)
-Pokemon Colosseum (GCN)
-Rayman Raving Rabbids 2 (Wii)
-New Play Control: Mario Power Tennis (Wii; mostly by reviewers who cannot seem to find the Options menu)
Also on DeviantArt, Rumble, DLive.tv, and the Fediverse (@freespeechextremist.com and @bae.st)