While there should always be that modern Lone Ranger aspect to Knight Rider, Mike and KI3T together are like a James Bond on our own soil and looking out for the little guy. These individual mission go on to have a huge impact overall. They co-ordinate with Sarah and Billy but really this is a buddy cop thing where one of them is ...a friggin awesome talking car.
In keeping with that, I see Sarah fully in the Devon type role and because of this her relationship with Mike is more strained than we have ever seen it. Consider it like the female M from modern Bond movies only this Bond can have actual sexual and romantic tension but at the same time is respectful (if occasionally annoyed) of the fact that she is his boss. However the more he is the field agent and the more Sarah is running FLAG the more remote the possibility of there ever getting together becomes.
I'd keep Billy as the main tech who confers a lot with Sarah since she knows KI3T inside and out. I guess this makes Billy Q in a way only the poor guy doesn't quite have the snappy comebacks down. Because hey, it's Billy.

Since some of the questions about Mikes past were basically answered at the end of the first season I think it's time to get into KI3T's past and for Mike to learn more about the legacy he's taken on. One question I think should be is KI3T something completely different from the original AI Wilton Knight and Graiman designed in the 80's or could this be the same AI only with no access to files and memories from his days with the original Michael Knight. Also exactly what has the original been doing since the 80's and how did FLAG get shut down to begin with? What ties might those events have on things happening now like the creation of a new KARR that is tied into Mikes past.
I would have season 2 be the time when the original series and the new one really begin to connect and the whole thing starts feeling still like something that stands on its own but is also a continuation of that story. Kind of like how the new series Doctor Who readily embraces its legacy and past while still blazing its own trail.