One issue will be constant fleet replacements. Of course there are costs to it. I would make the cost of extra fleets more gradual for every fleet, rather than the current, barely perceptible increases from 1 to 3 and from 4 up, with one huge increase from 3 to 4.
And another massive jump from 6 to 7.
The problem isn't even the big jump from 3 to 4, the problem is that the % size of the jump increases as your airline gets bigger.
A big airline running 4 fleets, and replacing all 4 with 1 fleet each, is going to be running 8 fleets for at least a couple of years. Airlines that big should have plenty of cash on hand for doing that, but it would still be much better if commonality wasn't so counter-intuitive, if there actually were economies of scale, rather than the opposite.
It would be much much better if commonality costs for each fleet were independent, with a discount if you only have 1 or 2 fleets for smaller airlines. First plane of a fleet = very expensive to maintain, thanks to needing mechanics/pilots trained for that plane, parts for that plane, etc, etc. But then more planes of that type add smaller amounts to total commonality.
One other issue around fleet replacements, and something that would be very desirable in general, is the ability to reassign pilots between classes for a small cost. For example, the obvious replacement for a large fleet of Sud Caravelles would be something like the BAC 1-11 or F28. But if you do that, you're going to have a lot of surplus large pilots, and need a lot of new medium pilots. If you replace a CV-340 fleet (3 pilots) with any of the newer 40-50 seaters (2 pilots), you'll have a lot of surplus medium pilots. The ability to take surplus pilots of one type, and pay a one-off fee to make them pilots of a different type, would be great. At the moment, the only options are to fire them and take the CI and morale hit, or pay them to do nothing for as long as it takes to have planes for them to fly, if you ever do.