Lots of them... sega is the master at killing franchises!
First the 1st generation of killed franchises that deserve another chance:
Master System:
Alex Kidd - The legend himself. I kidd you not, I find his first game - miracle world - better than Super Mario Bros. Great and colorful graphics, catchy tunes, excelent gameplay and a little bit of cool story. And a cute character, with big ears who also looks like a monkey! What else could we ask more? Too bad Sonic killed it, being more hip and kewl - because we all know that in the 90's you had to be kewl!
But it was not sonic that actually killed it. Sega was already torturing us - and alex - before that, with incredible crappy games, including releasing a horrible game that was actually not Alex's - a la Mario 2, only the game sucked balls (alex kidd in hi tech world). The one on the genesis - enchanted castle - was the last nail on his coffin. Now he's only part of history, serving mostly only as the 'did you know alex was sega's mascot before sonic" trivia everywhere! We miss you alex kidd, the man!
Wonder Boy - Oh, the best franchise of the master system era... with 2 good games and one GREAT game. In fact, so great it's to me the second best 8 bit game ever, second only to the legedary Mario 3 on the NES. Of course I'm talking about wonder boy, the boy wonder. The first game was good, an adventure island clone (even though it is the other way around, he was copied) with great action and a 5 second tune that sticked in my mind forever. The second one changed the formula completely, introducing some RPG elements, like money and items and puzzles, while maintaining the action. The third one - The Dragon's Trap - is a masterpiece. A huuuge open world (for the time) with lots and lots of cool places to go, lots of secrets and the best of all, 6 playable characters (which could be swapped on the fly), all with different abilities (one could fly, the other swin, etc...). Adding to that, some of the best graphics and sounds of the era makes this one of the masterpieces of the 8 bit era, no doubt about it. After that, Wonder boy had a shot on the Genesis with two mediocre games (again, sega killing it) and vanished from the gaming world. Another huge loss, and the closest to zelda sega ever got without actually copying it (or in other words, not counting the copycat Golden Axe Warrior)
Zillion and Psycho Fox were also cool on the Master System too, but they weren't actually franchises to begin with. So, even though they deserved another chance at the time, their time is over - no chance what so ever for a return.