Wonder Boy III: Monster's Lair (either Mega Drive or PC-Engine or better yet both!) - eliminated auto-scrolling screen and enable special weapons to last until you get another rather than last only a finite amount of time. This would make it feel more like a run n' gun game such as Contra rather than some auto-scroll arcade game. Also, choice to be either Leo or Princess Purapril from the start (or better yet, both simultaneously.)
Bikkurai Man (PC-Engine) - re-skin to restore it to the original Wonderboy in Monster Land (AKA Super Wonder Boy: Super Monster World)
Saiyukki World (Famicom) - same as above
Dragon's Curse / Adventure Island (Turbo Grafx / PC-Engine) - reskin to restore it to Wonder Boy III: Dragon's Trap (AKA Monster World II: Dragon No Wana)
Dynastic Hero (PC-Engine) - re-skin to restore to Wonderboy in Monster World (AKA Wonder Boy V: Monster World III)
Castlevania: Dracula X (AKA Akumajo Dracula XX) - either attempt to make it much more like the PC-Engine game as it was unfortunately inaccurately promoted to be a port of or just make it a more interesting pseudo-sequel. Level design and (most) of the backgrounds are so bland and uninspired and most of the difficulty is just from cheap cliffs conveniently behind you from enemy blow back, enemy spamming or both. (Then there is the horrendous entire level and a half you must keep the key without dying just to not get the bad ending.) Also, restore Maria, if possible and maybe add Annette as playable too.
Castlevania (NES) - adapt into Vampire Killer for the MSX2 (keep scrolling screen)
Super Mario All-Stars (SNES) - boot straight to Super Mario Bros. 2 which will be re-skinned to restore it to Doki Doki Panic (Famicom Disk System).
Castlevania: The Adventure Rebirth (WiiWare) - hack to become either Castlevania II: Belmont's Revenge and/or Castlevania Legends. Preferably the later as it could have used the Rebirth treatment, one of the worst CV's IMO.
Teenage Mutant Ninja Turtles (GCN) - hack to make it into a WiiWare style Rebirth of the classic Konami TMNT era.
Teenage Mutant Ninja Turtles (NES) - I don't really know what would be the best game to use as a base, but I'd love to see a TMNT game based on the Turtles in Space and Search for Splinter story arcs from the 2003 cartoon (in turn based on TMNT #4-7 of the original 1984 comics). All the Shredder and Foot stuff get all the love but this would be great stuff IMO. Maybe a multiplayer beat em up like Turtles in Time would be better, but i always liked the search and find aspects of this game and it needs polished from its many glitches. Instead of just the 4 turtles, there could be patches to plays as Casey Jones, Fugitoid, Usage Yojimbo, Zog the Triceraton and perhaps Leatherhead too. A few fights from TMNT: Tournament Fighter could stand in for the Triceraton Games if possible.