After reading a majority of people's ideas here, the theme which seems to repeat itself is return of more ninjas. While there is nothing wrong with Noob, Ermac, Rain, and Smoke, personally I think there are much better alternatives that Boon could bring back. Now before you laugh, just hear me out on a few ideas:

The return of Nightwolf, providing the next MK game takes place on Earth I believe he should return for multiple reasons. He was an original character with solid moves, and all around wasn't a hated character (unlike poor stryker). Also his moves mimick Johnny Cage's with their green shadows/energy. Personally I think the whole Johnny Cage returning to MK to make more movies is by far the worst idea I have ever heard of, and the only reason I ever used him was for his nut buster.

Fujin and Kai could return if MK takes place on earth, because Fujin is the protector of earth, and Kai wasn't said to be gone. Since he and Lui Kang were in the White Lotus society, along with Kung Lao, both Kai and Kung Lao could fight in MK together for their deceased friend. Another good twist would be bring Lui Kang's brother into the next MK providing he's not a clone of his brother, because I'm not sure if the MK world wants to hear another high pitch scream from the Kang family.

Sindel, if the next MK were to take place in Edenia then Sindel would be an obvious return to the series because she is the ruler of it. Many fans would be happy to see her return because she was very original and a strong character in MK3.

Jade and Rain, again if the MK series took place in Edenia then they could return, assuming they are in their homeplace. Rain I see less reason, unless they did away with Raiden. Jade however I would like to see return because her speed and her staff (Staff's are by far my favorite weapon) burnt themselves into my memory.

Ermac could return, if there was some reason for Kenshi to recieve help from someone, or if the creators could come up for an alternate reason for his return. Afterall he fought in MK3 to "prove his existence... as well as a warning that he will return as an unstoppable force in the fourth Mortal Kombat."

Reiko and Noob Saibot, they could return to either aid Quan Chi, or attack him, either way they could have a good setup for a story and I'm sure people would love some sort of official in game explanation of what the deal was with the Reiko/Kahn connection (or lack thereof).

These are just a few thoughts that have been on my mind...