What's gonna' happen to all those machine gunners in the modern era? Will they just upgrade to mechanical infantry?
Upgrade to mechanized machine gunners? It's far from rare to have them mounted on different types of vehicles now.
Regarding the unit balance, I really liked Empire Earths model, where you basically have a rock/paper/scissor system in each main group of units (air, land, sea) and then limited interaction between them.
A system like that means you need all 2-3 parts (depending on if you need to cross water to get to your enemy) supporting each other. You need an airforce to bombard hostile land and navy units to soften them up (which will work fine now that combat between units will take a few turns) and protect your own forces from the enemy airforce, but they can't capture any cities or completely kill off any units (scale down damage done based on remaining HP of the target to achieve this) so you need a navy to clear out the remaining parts of the hostile navy to allow your invasion army to cross, and land units to clear out remaining enemy troops and take the cities.
EE balance modified for Civ:
Other special cases:
IMO, the main problem with paratroopers isn't that they're weaker, it's the fact that by the time you get them you have other options that move so fast that you don't really get to the target faster anyway. Fix it by creating a modern version for them to upgrade to so they're not quite as weak as they are now and greatly increasing their range to maybe ~15 hexes and removing the need to have LOS on their drop site, but if there's a unit there they'll enter combat to the death with a significant combat penalty so that it's a risky move. Alternatively (or in addition to) the LOS requirement removal, add a spy plane with a good chance of avoiding detection (and thus not triggering an intercept at all, so they won't be used up) that can be sent to a specific area within range each turn to spy on it. (Fake edit: Actually, I guess spies could fill purpose and provide the LOS for a paradrop..)
Finally, they're air dropping using airplanes, so they should require an airbase (a city) to be able to use their special ability, but since you should be able to send several paratrooper groups at once, allow them to use it if they're within 1 hex from the city, but the drop range will still be based on distance from the city, and they should be able to move from city to city using those planes, just like any other air unit.
15 hexes may sound like a lot, but since they'd need to go from a city that's already a few hexes lost compared to the old system, and it would make them a weak unit that the enemy can easily counter by using machine guns, artillery or attack helicopters that counters even normal full strength infantry.
High production cost and a oil requirement would mean that they'd be useful as a rapid response force if a part of your territory need quick reinforcements, dropping in behind enemy lines and pillaging crucial resources (so place a unit there to defend it!) and for clearing a beachhead during an amphibious assault, but you'd still use regular infantry for the bulk of your infantry to keep costs down and strength up.
I'm not sure how to implement marines though, I don't see a role for them that isn't already filled by amphibious upgraded infantry. Maybe they could actually be a spec ops unit? I don't really think so, but...
They could be implemented as a scout upgrade, with 2-3 movement points with 3 LOS range, no terrain penalty, and the ability to helidrop x tiles away from anywhere (unlike paradropping planes, helicopters can land anywhere), useful for crossing water, mountains and other countries territory without declaring war. Since they'd represent only a very small squad rather then the significant portion of an army like regular units, they should have very low combat strength, but maybe have some limited ability to enter neutral territory too. Not really sure how to work that out though, maybe be able to stay hidden for 1 turn and then helidrop out/further in on the next turn, or hide if they're at least x hexes away from any hostile units, and give the regular scout a similar ability. It's probably better to just let spies deal with that though.
Regarding the actual topic title...if you want to use the set up condition for a combat boost, you could give the rocket artillery an extra movement point to compensate, but I'd rather just give bombers specific bonuses to artillery in that case, like pikemen get VS cavalry and AT guns get VS tanks.