The game would have to be severely upgraded for a modern release, given there were a lot of broken mechanics from the original. However I honestly don't see it happening as out of the spin off MK games that have a desire for a re release with the fans, Shaolin Monks is in the lead.
Why don't the ninjas have their stand alone game? Well Midway/Netherrealm probably never thought of it, had the time for it, or the ninja just didn't have that much of a deep story at the time. Mythologies Sub Zero is based off Bi Han. So maybe they could add something more deeper to the plot for said ninja, but games nowadays are a lot more work than they were in the PS1/N64 days (when Mythologies was released).
Another note is you would need a character that would sell the game a lot. Sub Zero was popular enough for Mythologies. I can say Scorpion would be another addition, but the rest, while popular in the MK verse, are that popular to the general consumer. I'm a Rain fan, but no casual is going to buy a Rain Mythologies. Nowadays, maybe they could release an episodic series via DLC only featuring the ninjas in a more retro form. So like anything from Trilogy pretty much, in terms of graphics and design, and that would go along with the Mythologies idea.
