Whilst I applaud the idea of hooks etc, I feel that the manta is just plain wrong.
The VTOL capabilities of the manta should be similar to contemporary VTOL jets - VTOL is only used when absolutely needed and chews through fuel at an alarming rate.
I am not sure if it already does, but flying with a hooked walrus should also cause extra drag and therefore more fuel use.
Thus a manta required to airlift a walrus would probably need an extra fuel tank (an item similar to an ammo box) in order to have enough fuel to be able to VTOL take off from the carrier, VTOL pick up the walrus, fly with the walrus hooked, VTOL drop the walrus, fly back to base and VTOL land at the carrier.
Maybe mantas should be allowed to take off with a walrus already hooked - such a mission could maybe be just about doable without extra fuel as you are doing one less VTOL maneuver.
This would also aid in control simplification. Most sticks will only have 4 axis analogue control, which does not leave enough axes for VTOL height control. For example when using an XBOX controller, you need to hold left trigger to make the left stick change from speed to alt, but it is not much use when you need it in a hurry.
Surely the solution is that VTOL is a separate mode - you normally fly like a jet (As in the original), then slow down - as you slow to below a speed threshold, an indicator lights up indicating VTOL mode is available. When you click a button, VTOL mode is engaged and controls change from jet style to helicopter style (speed control becomes alt, yaw remains same, pitch now controls forward/back motion, roll now controls left/right slip).
You pick up your load, gain a little forwards momentum in VTOL mode, and as you go back above the transition threshold, the VTOL light indicates that sufficient lift is available for normal flight - you hit the button and transition back to jet mode.