If you want to take advantage of Bioware's strengths, storytelling being one of the largest, you want them to have as open-ended a period to work with as possible IMO. That would make anything between Exar Kun and TSL a poor choice IMO.
As much as I hate to admit it, making the MMO KotOR 3 makes the most sense:
-There's a solid foundation of material to work with allowing for greater depth of setting. The previous 50+ years of Star Wars history as of TSL are fairly well-defined.
-Fans are familiar with this period and using it will allow the built in fanbase from KotOR and the various EU media to emerse themselves more quickly.
-The fate of the galaxy is still up in the air (barring the fact that we know the Jedi and Republic survive), as well as the fates of many of the key players of the era, including Revan and the Exile. This allows Bioware to shape your playing experience into a story of the player and his companions saving the galaxy while encountering a number of well-liked and identifiable figures.
-The Jedi Order and the Sith Orders under Revan/Malak and the TSL Triad have been decimated. Allowing the players to partake in the rebuilding of the ordes has the advantage that it can provide an excuse for why the Jedi and Sith are closer in ability to their non-Force sensitive companions than they would be in other periods, allowing for game balance and incentives to play other classes. A lot of the knowledge is lost or hidden and needs to be recovered, and repopulating the Orders will make the influx of adult Jedi more logical.
-The problem with placing the period X (X = ~500-3000) number of years after a hypothetical KotOR 3 is that it would undoubtedly reference lore that would have taken place in KotOR 3 pertaining to Revan, the Exile, and the "True Sith." Again, if we're talking about playing to Bioware's strengths, the depth of world in the MMO will be huge which means entire encyclopedias of new and established Star Wars lore will be involved. Unless a KotOR 3 SPRPG is being developed concurrently to be released around the same time as the MMO, some important details of the story of a future KotOR 3 would be spoiled.
The more I become convinced that our SPRPG will be overlooked, the more I want the MMO to finish the story Bioware began in KotOR. I'm becoming reconciled to it now. If Revan is the Illidan of KotOR and I had to go kill him as one of my endgame objectives, I could live with that. Let it be done with lest a KotOR 3 end up being forced to deviate too far from the games we know by the time they get around to it.