1) A Fire Emblem game set in any of the background story wars talked about in the games' prologues/intermissions. By now, there's several examples, including the Scouring, the original Crusade, and the Legend of Anri the Great. Anri's would probably be interesting from a gameplay perspective since the legend makes it explicit he solo'd his quest, which sounds rather out there in the SRPG setting.
2) We got 1800's Ace Attorney. Now let's go to the 1700's and have an Ace Attorney up against the Salem Witch Trials. Or perhaps go even further back and have an Ace Attorney up against the Spanish Inquisition.
3) Seriously, Zelda, give us the REAL Imprisoning War already. Enough fakeouts, alternate timelines, and trying-our-damnedest-to-make-our-fanbase-forget-about-this-backstory.
4) Since I brought it up in another thread; make a revision to the first Street Fighter. Not exactly a full-on example here, but since the first game is so obsolete it'd basically need to be redone from the ground up, it'd work more or less.
I'm of the opinion that Ninja Gaiden's continuity is kind of a mess and it's better to treat the games as loosely-connected. In that regard, I'm not sure what a prequel would really bring to the table, especially when Tecmo can't be consistent on if the "modern" characters are the same as the NES-era counterparts. Or the DoA counterparts for that matter. (Yeah, Zelda has this same problem, but at least they put a key event in their timeline that people want way back in the day.)
Speaking of which, joke idea: DoA entry where all the girls are underage, so your player character gets arrested for coming into contact with them. Haaaahhhhhhh.