Just looking over the campaign (I don't know how far you are, but it's got to be pretty far if you met the Shepseskaf)
mission 0: no warpouts at all so no problem here
mission 1: no warpouts
mission 2: the Cho, Cardinal, Idomeneus and Regensburg are all present at mission start and warp out after a full charge cycle. Some Ares jump in and out, they're fighters. Serkr Team (a group of next-gen shock jump corvettes) jumps in, takes a little while under risky attack to charge up, and jumps out. No problems here
mission 3: The Meridian is present at mission start and can (obviously) warp out. Same goes for her escorts. I think the only potential for a real problem here involves the Yangtze, which might be allowed to jump out very soon after jumping in depending on how the mission script plays out...but most players will probably never even see her, so I'm not sure.
mission 4: obviously no warpouts
mission 5: no capship warpouts
mission 6: the Redoubtable is present at mission start and warps out on a full charge. The AWACS can jump out really soon after jumping in, but they're very small craft. The Valerie doesn't have a chance to jump out after jumping in, nor does the Indus. The Atreus is a next-gen combatant with a sprint drive. No problems here.
mission 7: no capship warpouts
mission 8: no capship warpouts
mission 9: This one I'd question why the GTVA didn't jump one of its warships clear. Presumably they were unwilling to risk abandoning the Agincourt, though it's pretty negligent that they didn't manage to get even one jump-capable ship off the deck - the warships themselves were probably still in charge cycle after their last jump. No capship warpouts, however, except the Agincourt if you fail the mission - it takes quite a while to charge up. I'm less happy with this one but I don't think it has glaring issues.
mission 10: the Indus and Yangtze won't try to warp out at mission end, presumably because it's a situation just too critical to abandon the fight. Torpedo Two jumps in and gets shot to **** before they have any chance to jump out, unless you're really good. The Hood jumps out at the end of a full charge cycle. The Medea jumps in and doesn't get a chance to recharge before being shot up. Seems fine.
mission 11: the one I'd worry about here is the Hesperia, but I'm not sure exactly if or when it jumps out - it might be a bit quick. Possibly a problem here, but it's not tactically relevant.
mission 12: nuttin big
mission 13: the Spectre is an AWACS and has time to charge anyway; the Shepseskaf has something seemingly akin to a sprint drive setup, which makes sense given how excellent Vasudan reactor design has always been. No big problems.
mission 14: jump dynamics are obviously a big deal here, but the Antenor and Norfolk both get caught on the down end of a charge cycle, and the Carthage has to use her sprint drive to escape. Seems to play by the rules.
mission 15: none of the UEF ships that jump in are able to charge up and jump out, except the Indus, which is the first to arrive and which gets to spend a large chunk of the battle in the relatively safe back rank. It doesn't have a nav fix ready either. A large number of GTVA ships are able to warp out, but they all had time to charge up. Seems fine. Mister Cuddles might break the rules of course 
mission 16: heh.
All in all the rules seem pretty consistent. The one I'd worry the most about is the Hesperia...checking its departure cue, though, it doesn't have one, so no problem there! After that the biggest problem is the Yangtze in Post Meridian, which can, if the mission proceeds along a certain route, jump out immediately after it jumps in. That's a clear continuity error, but it's unlikely to happen.
This is the same kind of check we ran through multiple times during development.
I've beaten the game already, so no worries about spoilers.
I MIGHT be somewhat misremembering a few instances, but even then, there are way too many for me to cede my argument, here. At all.
Now, here is how I imagine it working:
1) The power requirements for charging up a jump drive scale up X-squared; the larger the mass doing the jump, the larger/more powerful the jump drive needed, the more power (on a scale of x-squared) needed to charge it. Thus, a fighter can recharge its small jump drives pretty quickly, but a destroyer takes much longer. However, that doesn't mean that a larger ship will always take longer than a smaller one--not at all. It's just POWER needed; more efficient, powerful, larger, numerous, etc. generators/reactors can speed up this process along similar lines. Thus, a Raynor can still recharge its jump drive faster than a small destroyer, or corvette, from the Great War or maybe even Capellan era, because it's reactor/generator output is vastly larger/more efficient.
2) Navigational computing does NOT scale up like power requirements; it's purely linear, or maybe even less. Gravity affects lighter objects more than heavier ones when inertia comes into play, and ships still need their normal engines to travel through subspace, so there's definite inertia there. Further, unlike with fighters/craft, navigational computers can be very large and more powerful, so calculating a jump for a frigate like the Indus should take very little time, relatively speaking. Certainly no longer than a minute. This is backed up by canon, if I remember correctly, as the delays for a ship to jump away/escape are always mentioned to be ones of needing to recharge or repair engines, NOT calculating stuff in the navigational computer. This is further backed up by AoA--the Oresties can't jump out for ten minutes because that's how long it will take to RECHARGE the jump drives. Even in the gravity well of saturn (or wherever that place is), and under heavy attack, calculating the jump itself is never even mentioned as a difficulty or the limiting factor. Same with the Duke, even though one can make the claim that the Vishnans helped that part along.
This is further backed up by how having multiple intrasystem jump drives works in practice. You can calculate a new jump very rapidly; having the second drive means that you have a second, fully charged drive available to use ahead of time, which is why it works. Once again, WiH backs this up--the Atreus, in the mission to defend Rhezus (sp?) Station, makes several jumps in rapid succession with its dual-drive system, even while engaged in combat the entire time, and--this is notable--when the Atreus had no ships in the area to counter it, and was planning on staying there at least long enough to wipe out the station and its defenders, it was only when massive reinforcements showed up without warning and against expectations that the Atreus decided to jump out--which it did successfully, in less than 30 seconds. This is a massive destroyer we're talking about here; one that has been engaged in heavy combat constantly even before it jumped to attack Rheza, was engaged in combat during the attack, was engaged by massive UEF reinforcements, was in low Earth orbit, and was maneuvering significantly. And it still calculated a brand new jump, without warning, in seconds. It wasn't even a crash jump, either.
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Further, it's established that you need normal engines to be able to actually do a subspace jump. The whole deal with the Yangtze doesn't make sense, then, when the stated reason it couldn't jump was that it's engines were completely down, beyond quick repair, and thus had no motive power to actually use to enter/traverse subspace. The Yangtze then promptly turns around and charges the Imperieuse, engines seemingly working just fine. Its captain confirms that when she orders the maneuver. So unless I misunderstood the dialogue after hearing it twice, the Yangtze couldn't jump because it's engines were totally down, but it then used its engines to turn around and charge a destroyer, without any known or implied consequence to the engines. Erm...what? Did I miss something?
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Additionally, it seems that you can't jump to a place right next to a jump node, or at least not easily (heavily backed up by canon). How one can overcome this isn't explained; it might be better nav computers, better jump drives, much higher power output required, or strong enough structural integrity to withstand whatever forces/instability comes from the act. Additionally, it seems that intersystem jump drives are separate from intrasystem ones, to the point where it seems that you can't use an intersystem jump drive for an intrasystem jump. There are many possible explanations for that, but I don't think we need to go into it.
