The inspiration for this came from Kirith's Capital Ship Gap post. Now with the caveat that I do not lead a mom owning alliance (although I was surprised at the number of capitals that came out of the wood work when we operated in low sec against that pirate tower), Here are some observations from afar:
The proposition: The biggest problem with MOMs is that their signature feature - clone vat bays - do not apparently get used very much. The main reason for this is that they are pre-engagement items and they take logistical planning to use. The second problem is that they have limited capacity in the age of blob warfare that is the EVE capital battle field of today. Since they can only have 4-5 battleships in their ship maintenance arrays this poses severe limits on their usefulness in supporting any serious operations and I assume renders them only useful for HAS squadron support. I would like to propose two changes to make this signature feature from the realm of "novelty feature" to the realm of "raison d'être":
1) increase their ship maintenance array to the point where they can at least support a heavy squadron (i.e. able to stuff at least 10 battleships in their ship maintenance array). 20 would be better but at least 10. Anything less is simply not sufficient to a modern EVE fleet support role. Their current configuration from what I can see is only useful to a black ops task group or a HAS gang and those are mobile enough by themselves as it is not to necessitate the use of a Mother ship for rapid re-deployment.
2) Introduce a new form of clone bay module - Emergency Medical Clone Bay I (or something like that). When part of a fleet, allow ships in the squadron/wing/fleet (depending on the position of the mothership in the fleet structure) to register with the mothership. Then if pilots who are registered get podded (or self destruct) instead of appearing at their medical station (way back where their base is) they would apear in the mothership. This would allow the mothership to act as a true forward logistics unit for a fleet enabling it's pilots to get back to the fight as quickly as possible. It would also be synergistic with the previous suggestion.
These two changes put together should allow motherships to make their signature feature useful enough to become usable on or near the modern EVE battlefield.
With regards to the fighter bombers and supercarrier concept. I would advise CCP to take the time and design a new ship class for this concept and simply not convert any motherships to supercarriers.
Problems common to Motherships and Titans:
These ships are supposed to be the back bone of capital fleet operations. At least that is what it looks like from afar. However for all their massive scale they do not scale up to their roles very well. They however have two big problems. Their facilities do not scale well to the size of modern EVE fleets. The Titan has less problems in this regards than the Mothership. Since it can portal quite a significant number of ships (the jump portal being one of the 3 signature elements of a Titan) And the doomday weapon whether in it's old or new configuration is significant enough to make it a presence on the battlefield regardless of any other feature.
Due to it's portal generator and ship doomsday weapon, personally I'd make it's ship maintenance capacity LOWER than a moms (more to the point - make the MOM's higher than a titan's) and would not allow it to fit any new fancy clone module just the old pre-planning one.
The other problem with titans and motherships is that they necessitate the pilot to remain in them quasi permanently which basically kills any non-titan/mom applicable ship skills they may have acquired prior to becoming a Titan/Mom pilot. There needs to be some way of parking a MOM/Titan in something a little more substantial than a large control tower. They are just way too vulnerable on the modern capital infested battlefield.
Someone else will need to come up with a reasonable solution for that allows a titan mom pilot to jump in a rifter from time to time without out having to worry that their titan will no be there once they get back to it without having to dock the titan/mom in some invulnerable station. Maybe having an internal capital ship maintenance array as being one of the tier 3 upgrades to an outpost or something like that.