Even from a role-play perspective it would not be uncommon to have different space and away teams. Picard didn't always go down with Riker - and Riker almost never went down on a mission with Picard as it was his job to run the ship when Picard was away. Likewise Geordi, Data, Worf, and Crusher didn't go on every away mission either. It would not be unreasonable to leave your First Officer behind since the Captain must go on the missions in the game.
It's too bad the missions aren't more BOFFcentric in that sometimes you need to take a Medical, sometimes and Engineer, sometimes a Councilor, etc.
My department heads almost never leave the ship. It's bad enough the Captain is going on away missions as it is, so there is no way my First Officer is coming with me.
...As for my away team, I've more or less assembled an "A-Team" of what I like to think are MACOs. All "Very Rare" officers, all 'Commander' rank, with the best gear I can afford them. 2 Engineers, 1 Tac and 1 Science. There is no way I'm beaming my 3-star backside on to a Borg-infested planet without a crack squad of commandoes to guard me!
My CMO will simililarly only leave the ship where the chance of needing absurd amounts of healing is high. Otherwise, I'll send one of my other Doctors.
I use different bridge crews for each ship (I switch ships frequently) so a some point during the day all my 14 BOs are bridge. I tend to stick with the same away team (2sci and 2eng). Very early on I replaced me original "common" officers with identical very-rares so all of them can go topside if I have trouble with a mission using the mains.
I'd like to do this more, but what keeps happening is I get so used to my ground team that it feels wrong to replace them. At the same time, I hate having to re-train new BOffs for Space when the group I started out with does just fine. It doesn't help that I refuse to buy BOff slots.
By end-game I definitely do have some space-only and the occasional ground-only BOffs, but I've never fully divided them.
My ground units are less so, although I've still got a few humans kicking around.
The key is traits - one of the human traits is a space repair bonus (I forget what its ground effect is), so its them or the borg shield repair bonus. on the ground those bonuses are less useful. off the top of my head, I've got a borg and bolian engineers, a trill science officer, and until recently, an andorian tac (now human)
This describes me, too. I've got 13 bridge officers (was 12 for a long time, but got annoyed that my photonic officer didn't show up on the bridge, so I commissioned my KA Borg to get rid of that generic officer).
I don't separate them for space and ground so much, but I do have two different space sets - one for the skills I'll always have on an escort, one for the skills I'll always have on a cruiser, and I have them set up to cover variations - for example, I can switch my Gorn and Breen back and forth to have either APO3 or APB3.
Then I have two separate ground teams. One is three engineers and a science officer, with miniguns, engineers with turrets and drones, and the science officer with a couple AOE attacks instead of straight heals. Capacity shields, polyalloy armors. They're my shock-and-awe team, and pretty much anything ceases to exist against them.
Then I've got a second team, 1 tac, 1 engineer, 2 sci specifically set up for fighting the borg. More heals, defensive powers, pulsewaves, plasma shields, energy dampening armor, and remodulators.
I've considered upping myself to 15 boffs and setting up an anti-devidian team with psionic shields, but currently I just use two of my engineers with the science officers from my borg team.
My Boff set up hasn't changed much since beta being nothing but 4 tacts for ground, but I used to run 2 separate space teams depending on the ship I was in. Eventually though I just made an alt to fly the X in so my main's Boffs are static. 2 have dual duty in space and ground but that's the only overlap.
But I agree with people that I have more Boffs then I know what to do with. 3 Orions, (1 each), Tac Vet, Borg ENG and SCI who all work while my Reman, Breen, EMH, Android, Caitian all stand there and look pretty. I may be forgetting a few of them as well.