There was a resolution to the Batarian and Human rivalry of sorts in my game... Despite all of the animosity between them, Shepard did various things to help the Batarian refugees on the Citadel, taking the time to talk to one of them who survived the destruction of the Alpha relay (it's a lot more personal between them if you completed Arrival) and then finishing it off with Balak. Despite his hate of humans, his species being put on the endangered/near extinction list, he has no choice but to put aside his feelings for humans and pledge what's left of the Batarian military's support to fight along side the humans against the Reapers instead of sabotaging them like they were before. There's also a Batarian on Omega, forget his name, who ends up respecting Shepard and even tells him "just know that there's one Batarian who doesn't hate humans."
In fact, now that I think about it, all of the species had their small to large moments in the game, they just didn't have the spotlight on them equally, which I think is fine. But as I said before, if a Batarian squad mate was going to be introduced, the best time would have been during the events of ME2 where it was ONLY humans on the line at the time. Imagine if you had a Batarian squad mate join you at that time, now THAT would have been an interesting companion to have at a time when the enemy was hunting down humans.
As for Javik's character... he was a lot different because he didn't bother getting to know the crew, he offered another outsiders perspective but what he was most important for was giving you background information about everything that happened with the Protheans and the Reapers... and some very funny moments.