One of the nice things about this is that the player can choose how much these ships invest in ther carrier or combat capabilities. You can fill an Odyssey full of bombers and related hullmods, give it it balanced weapons and a light escorts or turn it into a full fledged assault ship without any fighters.
I get what you are saying here and that's kind of my point actually

. I really do not want a system that essentially makes me choose one or the other with those type of ships. The entire draw of a ship like the Venture is its tactical flexibility
during combat not in just in how it can be set up beforehand. Re-specializing a ship costs time/supplies so when I go for a ship like that I expect it to be a jack of all trades so to speak.
I know you also meant that the third option from a hard specialization in either direction would be a "just right" weapon loadout that included assault weapons and fighters, but my instinct here tells me that attempting to balance that approach would make the middle ground loadout either the only viable choice or so poor in its performance its completely undesirable.
The biggest issue here is that making the carriers's CR drain from deploying fighters forces a shared resource pool between two very different features of the game (deployment and in-combat fighting) with no real benefit other than a false sense of simplicity. I say false because the cost of deploying a ship before combat should always be a separate resource from the weapons it uses during combat to prevent unnecessary convolution, confusion and balancing issues. Too many different things draining one resource and you will never seem to have enough of it and that resource becomes way too important. Thats on top of the issue that changes made to one system absolutely require changes to the other system. In my opinion, CR as a mechanic is already dangerously close to being too integral to too many features for the health of the game.
Fighters are not an exception to this rule (at least in my mind) and keeping a separate resource for their deployment (replacement chassis, their own CR bar per wing or something totally new) is essential to making carriers something fun to use rather than a headache because it has too many drains on its single resource pool to be effective
when compared to the basic assault ships.
My solution is actually just to keep fighter wing CR separate like it is now so each fighter has its own resource pool, just integrate that mechanic for fighters as a weapon mount rather than a ship.