Nimitz
I'm not sure I fully follow how the carrier fleet is meant to work. It has, to my eyes, very odd maintenance life, deployment time, and fuel capacity.
At a minimum I aim for my carriers to be able to fully re-equip their squadrons for every two months of deployment time. I rarely see it necessary to equip them with more than twice for every month of deployment. So if I want a carrier to be able to be deployed for 6 months then it should be able to fully refuel and rearm it's entire complement at least three times, and at most twelve. Regardless of the option I pick, everything is designed around that maximum engagement potential. Right now though your carrier can only be on station for ~2 months despite having a refueling capacity for its combat wing for ~89 engagements* with a rearmament capacity of only 5 engagements for it's missile armed fighter craft. ^ I think you're okay on missiles but you're carrying way too much fuel. Unless the Nimitz is meant to act as a fleet tanker for support ships? Personally I'd suggest having a dedicated tanker and/or fleet support vessel for that, but there's nothing wrong with combining the roles. However, maintenance life is still a problem no matter what's decided about its tanking capabilities.
* Total fuel consumption of your entire wing (all 43 craft) is ~220k. I assume an engagement lasts exactly 28 hours. Invariably there'll be shorter ones and longer ones, but let's assume total exhaustion per engagement as a baseline. I also assume that the Nimitz only uses fuel for 6 months (which is the intended deployment time), and undertakes no other tanker operations.
^ Total missile consumption of the Buffalo complement is 72 missiles, and the Rhino is 24. With stocks of 360 and 120 both divide nicely down to 5. With a maximum deployment time of six months this should be fine. I wouldn't advance with this carrier too far though, not without an ample number of colliers bringing missiles up to the front.
If you're going for 5 engagements over a six month deployment I'd recommend altering your fuel capacity to ~4. 5 million. That'll give you five full fuel resupplies on your fighter complement (1. 1 million), give the Nimitz enough fuel for six months (2. 95m), and leave you with a couple hundred k reserve for emergencies (495k). Obviously if it's the fleet tanker you'll need to adjust those numbers, but 20 million fuel is a massive investment; and I can't see why you'd take that risk. The extra space would be better used to up maintenance life, or add more armour. I prefer my ships built to withstand absurd levels of punishment (15+ layers of armour on a capital ship), but provided you know what you're doing less armour isn't a big deal.
You only need 93 spare berths on the Nimitz. If you want spare to take survivors (I don't think it matters, but I like to include spares anyway) then that's fair enough. You could probably reduce to 150 spare berths to save on space though.
I know the thread seems to suggest that Gauss was the way to go. Honestly though, I think CIWS is the better option for this, particular, carrier. My thinking is that given its relatively low armour/shield levels this isn't a carrier I'd expect to see near the front, much less providing covering fire for a fleet. If the Nimitz is called upon to give supporting fire then it is too close to the action and you've either made a pretty significant mistake (given the amount of fuel it's carrying), or your design is lacking in armour. CIWS is good personal protection for a ship that isn't likely to see combat directly. Gauss Cannons and the like are better suited to support ships between the carrier and the enemy.
Fighters
I'd also replace the Tyrant missile on the Rhino with the Tyrant II, it's a far superior missile. Given the short range of the Tyrant I would consider stripping the Rhino down dramatically. It needs to move to within 1mkm to launch, so it either needs to be your fastest fighter or you need a more long-ranged version of the Tyrant. Also, are you putting engineering spaces on your fighters? Pull them. They've an engagement time measured in the hours. They'll die or be recovered before they break down.
You don't need magazines on your light craft if they're mounting box launchers. The missiles are already in the tubes, and you can't reload box launchers except on a carrier or on a planet anyway.
You may want to consider an expanded scouting complement, and potentially even remove the sensors from the Nimitz altogether. The EA-6 has as good an active sensor as the carrier, and it has the added advantage that it won't give away the position of such an important vessel by turning its active sensor on. I'd suggest three EA variants; active, thermal, and EM. Put half a dozen (two of each) on the Nimitz. I like to RP a little, and by the looks of it so do you, so I'd suggest (purely on the basis of RP - it isn't necessary) that a much smaller thermal and EM sensors are included on the Nimitz instead purely for navigational assistance. I'd stress, again, however, that this isn't necessary.
Have you tested the F-54? I tried anti-missile laser-based fighter wings before, and found box-launchers from fighters were far more effective. Unless combat testing or ordnance manufacturing capabilities suggests otherwise, I wouldn't be so quick to retire the F-44 to local defence duties.
I'm really liking the designs, especially the little bit of background you put into each one.
Edit: Decimal points man, they're important. >. <
