I have a picture somewhere of a tender proposed for the Sea Master jet flying boat which just hauled the aircraft up an artificial beach. If you were willing to design your daughtercraft to be launched a recovered this way then it might be easier than cranes. We needed to be able to handle daughter craft with propellers and normal hullshapes, however, so that wasn't an option in the mothership study.
RNLI lifeboats would provide a model for a daughter craft compatible with an artificial beach - waterjet propulsion, strakes to support the aft end, rubbing strips / rails on the three contact points (centreline keel and side strakes) and a lot of local structural reinforcement. Of course, as you are operating from a mothership, you could trade off some endurance for additional structure.
Handling when pulled up the beach would be by some kind of trolley (a big one!). But this would never go near the water and could perhaps use lots or rubber tyres on a guideway rather than be a true rail system to avoid the usual concerns over rail alignment on ships.
The nice thing about this is that, apart from the round-down for the beach at the stern, the ship would be relatively conventional and most importantly would not need to dock down with the resultant survivability issues - those heavy lift ships sink by accident occasionally! That being said, there are some solutions (massive sponsons).
RP1