For the systems it covered, Wii VC was pretty amazing. TG16 and Genesis were especially well covered too.
I think the major holes in the library were:
-Mother/Earthbound (rectified on Wii U)
-Super FX games: Star Fox, Stunt Race FX, Yoshi's Island, etc
-Zapper/Super Scope games (semi-rectified on Wii U)
-SVP/Sega CD/32X games: Virtua Racing, Sonic CD, Lunar, etc
-Quintet SNES creation trilogy: SoulBlazer, Gaia & Terranigma
-Konami NES/SNES cute 'em ups, ie: Parodius & Twinbee games (semi-rectified on Wii U)
-Konami Genesis games: Hard Corps, Bloodlines, RKA, etc
-Game Collections: Mario All-Stars, MM Wily Wars, NG Trilogy, etc
-Tecnosoft Genesis games: Herzog Zwei, Thunderforce series, etc
-western games in general: only Factor 5, LucasArts, Activision or Interplay were present at all
-Arcade games in general: only Namco in Japan really tackled this comprehensively, no DK/Jr/MB is a bizarre omission
-3rd party N64 games in general: Mischief Makers, Goemon, Snowboard Kids, etc
-Too much MSX stuff to count, also never made it overseas
-Later Neo Geo games like Garou, MS5, SSV, etc (maybe a RAM issue?)
There were some other obvious missed opportunities besides those (Pilotwings 64, Ys III, Ranger X, Guardian Legend, Clash at Demonhead, Secret of Evermore, Magical Chase, Waku Waku 7, Nintendo World Cup, Warsong, etc, etc) but those seem like the bigger ones. More localizations like what Sega did for MW4 would've been great too. SE in particular could've banked from this even if they only used already complete localizations from rereleases and remakes for it (FF2/3/5, Tactics Ogre, Front Mission, Romancing SaGa).