Run number one: EDI and Javik
A lot of the differences are simply the difference between Tali and Xen. Not sure any are related to team mate specific changes to account for the lack of Tali, although there was a small bit of back and forth between Javik and EDI.
-When looking at Rannoch through the docking tube, Shepard says Tali would have loved seeing it, and Joker comments that we have to win this for the sake of Tali.
-Xen somewhat criticizes Gerral for his attack plan, but then pats herself on the back for her technological breakthroughs
-Xen appears in the ops center after the fight is over and basically rehashes Tali's lines. She then cloaks before the next fight begins.
-Xen has a funny line about hacking Geth and having them serve her drinks (EDI is not pleased with Xen's attitude towards Synthetics.)
-Xen is none too pleased that Gerral is shooting at the Geth ship while she is on board
-Shepard promises to keep the engine running for Xen as they flee towards the fighter, but she doesn't show up until you get a view of Shepard & Co. in the back seat.
-Back on the Normandy Xen expresses regret at supporting the war
-Joker's post-mission dialogue is rather different. He talks about "our new alien allies" as if we had not been to the migrant fleet before. I think the assumption here is that the only reason Tali would die is because you didn't do her LM.
Team mate banter:
Never having taken Javik on this mission before, I don't know how much of his dialogue is related to EDI, and how much he would say anyway. But I did find out about the Protheans sparking a Supernova to wipe out the Zha'til. EDI commented that that is not an option in this case, to which Javik replied "not yet." Javik's post-mission dialogue did not differ, although Shepard's comment about him mentioning AI problems made more sense now.