It's unlikely, and there are good solid reasons for it.

You have to understand that the creative team behind the arcade MK's (MK1, MK2, MK3, Ultimate MK3) did not directly work on MK Trilogy. As a result, the team has not come to see it as a "true" MK game. Sure, bits and pieces of it are referred to here and there (Khameleon and Chameleon's appearances in Armageddon being a prime example) but by and large, whenever Midway/WB/NRS re-releases the "classics" they pretty much just mean the 2D arcade games, and UMK3 was the last of these.

Also consider that the arcade games had higher resolution, and thus look better on a modern high-definition TV. Johnny Cage and other MKT characters and moves were only produced in low-resolution. So the options would be to either include the lo-res game, or going back and getting higher resolutions of those sprites. The second of these is simply too much work for something that would probably fetch no more than $5 in the PSN Store/Xbox Marketplace and not a good business decision.

This is why MKT will likely be forever ignored by these compilations and never ported to the current or next-gen systems.