I'd like to see SC2 prequel sequel combo being made. It would be nice to be able to interact with the races previously wiped out by the Ur Quan / Kzer Ah. (Either in their doctrinal SC2 war or under orders from the Dnyarri when the brown Ur Quan were conquered).
Perhaps the machinations of the Orz in the present day could cause a defect in the Quasi space portal spanner so that each exit from Quasi space is in a different time period of the Galaxy.
This way you could have the time of the Precursors, the Dnyarry conquest, Star Control I, (near) Star Control II and perhaps some possible times one where you succeed your main mission, one where you failed. In the near Star Control II time, you might have a chance to warn the Arilou of that time period of the experiments the Androsynth plan to do leading to some Androzynth survivors. Saving perhaps the race that warned the Druuge in order to get their help in some way.
Each time period could have its mission. The Precursor could need something done for example. In exchange, they give the player a key piece of technology that will help the Taalo make the device which makes one resistant to the Dnyarri. The mission in the Dnyarri time period could be crucial to some event that must happen in the SC1 or SC2 time period etc.
A submission could be to get help from the Taalo in order to recruit the original brown pre-Dnyarri Ur Quan to steal some weapon technology from the Ur Quan and/or Kzer Ah.
The Pkunk said that the Ilwrath were perfect beings in their previous incarnations. One of those times could have that incarnation of the Ilwrath. Perhaps see an earlier incarnation of the Druuge before they were corrupted by one of the artifacts they have in their home world in SC2.
Along the way the Captain could get volunteers of each race that got wiped out (and/or other past race) and restore their civilization in the future by creating colonies for them. Maybe see how the Maelnum react when they encounter the race that previously tried to cheat them come back from extinction.
In the SCI time period (or earlier in the Dnyarri time period), the player could attempt to find out what artifacts were destroyed from Earth by the Ur Quan when Earth was conquered and why. In the Dnyarri time period perhaps the race that became the early Arilou and Maelnum did experiment in splicing the dna of the defeated Dnyarri to Human dna and their own leading to the creation of the mind controling Syreen race. (The Maelnum after all probably collect biological data for a customer (probably Arilou) who tamper with human dna).
The cloaked race that the Maelnum kept mentionning in the SC2 could be instrumental in solving the Orz quest.