That's essentially what many of us were hoping would be the case, a while back... It should be relatively easy to make genuinely interesting military-based missions, because they're so diverse in reality. There were lots of fun sorties I remember from way abck in the days of the Janes series of flight smiulators and '
EF-2000', to say nothing of the '
Wing Commander' games and, of course, the ever-beloved '
TIE Fighter', which could also be fairly creative in terms of both scripted and coincidental events, along with basic missions priorities.
They don't have to include actual combat. Recon would be
very fun, because it would involve trying to be stealthy and plot your way around enemy sensor nodes. Anyone remember the old '
F-19' Microprose game and how they did that in there?

I'd love to be able to undertake escort missions for NPC strike packages, too, which could be very thrilling. Even hiring NPCs to escort
you seemed like an incredibly basic feature Frontier could yet install (not all ships can physically launch fighters, after all). All sorts of stuff...
And if they ever get around to properly armoured combat ground vehicles (the present SRVs look like glorified scientific scouts, at the most), Frontier could learn wisely from Microprose's two '
M-1 Tank Platoon' games, which had lots of really fun ground-based missions. If I remember correctly, they could even be procedurally generated, to result in thousands and thousands of potential different missions.
Right
now, there's nothing stopping them from giving us missions with surface targets in, either. God knows why 'skimmers' can't be targetted from a ship (they damned well
should be able to be), but I'd love to be able to use mine for interdiction and search-and-destroy missions, like the Microprose and Janes helicopter gunship simulators used to do. Frontier coudl learn a lot by reading through their manuals and reviewing old footage available on You Tube of the mission briefing screens!
What you describe would effectively be like acting as a dropship. There's a simulator of the Russian Hind gunship you can get on Good Old Games (titled '
Hind') which simulated going to a certain location as part of the missions (it would sometimes be the primary objective, sometimes not) and briefly landing, whereupon your small contingent of troops would disembark. You'd sometimes have to make sure the Landing Zone was pacified before doing so. Then you lifted off and either went to the next target or back to base. One of the later '
Silent Hunter' submarine simulators, set in the Pacific, did something similar, where you launched or recovered divers, I think.
There's no reason why we couldn't have something smiilar. Especially since we actually
have a ship which is literally called the Federation Dropship.

It's just a case of constructing the mission so that your ship has to either land or stop (or merely decrease speed) at a pre-set designation. It would be easy enough to have missions where you ferry troops or vehicles in that way. Evolving it further, so that you can then take direct control of a surface vehicle which disembarks and has to take care of its own surface combat missions (which could include a series of different objectives, ranging anywhere from recon to escort and strike), should be simple to do.
The only caveat with that is that it would really need Frontier to give us NPC allies and 'wingmen'. Games like '
M-1 Tank Platoon' and '
Janes Navy Fighters' always had at least three other NPC team members you could send commands to (including selecting formation types). '
EF-2000' evolved that, somewhat, by also making it so that you could select the EMCON level... 'Emissions Control': This would limit or open up the kind of communications you would be setting, so that you could be emitting any signals you wished when in friendly territory, but knew you had to cut down on it in enemy territory, otherwise they might stand a better chance of detecting you (even when flying at an extremely low altitude). It also dictated whether you and your wingmen would be allowed to use things like active jamming, because that also involves emitting signals. You'd have to choose between survivability and 'stealthing up', which made things extremely fun, the closer you got to a coincidental combat patrol flying around your target...

Was it aware of your location? Were they tracking you? Did they have a lock? Then maybe they'd turn away at the last moment and you'd breathe a sigh of relief... They didn't see us! Woo! No, wait, they're turning to engage -
argh! Have you been allocated an escort? Maybe you could turn and fight, but it would use up too much fuel. Vector your escort in to help you out!
Which brings in the question of engagement protocol. It would be nice, in combat missions, if we had to abide by certain rules of engagement. I remember as far back as '
F-19' that this was dictated by whether the political state between two factiosn was peace, cold war, hot war and such. So, maybe it'd have to be like '
Top Gun' and, even if someone has a lock on you, you aren't allowed to fire before being fired
upon. Doing so might fail your entire mission. Would apply just as much to our ships as any surface vehicles. Maybe we'd enter a system undetected, make it to inserting a ground vehicle, but then suddenly find ourselves surrounded! Do you shoot your way out? Do you try and manipulate them into shooting at
you, knowing you could call upon support and then wipe them out?
Stuff like that, diversity of choice and giving the player an array of
choices which can dictate a mission's outcome, makes them feel empowered and like their decisions truly matter. It opens missions out, so that it no longer feels like painting-by-numbers.