I personally have Alpha 1 talk some, because, well, it's weird when Alpha 2 responds to Command instead of the flight leader, you know?
Mostly, though, I took my cues on character work in Freespace 2 from playing Homesick and Derelict. People don't have to interact with Alpha 1 for them to be good characters and likeable, or hateable (is that a word?) as the case may be. And you can give more characters personality then you might think.
Even the bit characters of Cleaning Crew have some personality. The commander of the Actium, for example, instead of saying "Good luck, pilots." at the end of every briefing where you work with the Actium says instead "Skill, pilots." I admit I blatantly stole that from BattleTech, but it still makes the Actium's CO different from the regular briefing guy. Or for another example, Alpha 1 of the Blue Lions makes references back to "The Romans Blunder", and I'm probably the only person alive who's ever included the original FS2 Alpha 1 as a character seperate from your own and made them female.
I name characters. I'm a writer. All my characters have names, including Alpha 1. The names, for the most part, exist only in my head. If I ever hammer the incoherent story ideas based on Cleaning Crew that are sitting on my harddrive into real story, you'll find out what all the names are. But quite a few of the characters in Cleaning Crew have their full names used at least once, four or five, more then I can remember in any other campaign.
It's also untrue you really need boring missions for character development or advancing the plot. The same can be accomplished in fairly active missions: look at some of the missions Shrouding The Light for examples. It is certainly easier in a calmer mission, but they aren't, strictly speaking, necessary.