Okay, so I've tried and tested the Manta (M) out a little bit.
It was fun. Really fun, actually. Very refreshing from my usual piloting of Capitals and some Cruisers.
Here was my loadout:
1x Crossbow Heavy Bomber (Mayasuran Prime ships get a -2 OP cost to bombers, it's hidden in its description)
2x Ion Cannons, front energy mount
2x Railguns, front ballistic turret
1x Dual LMG, central turret
2x Reliant HMG, rear turrets (from SWP)
ITU
Rest OP in vents
First thing of note is that the Crossbow is, effectively, a Fighter-Bomber. In addition to its Gorgon missiles, it also has a twin energy weapon thing on the front. You can actually deploy the bomber against other bombers and fighters and they'll indeed shoot them down.
Second thing of note is its maneuverability special. Unlike the regular Manta's Burn Drive, the Manta(M)'s drive has two charges, lasts a shorter amount of time, allows for a little bit of turning during the burn, and allows the Manta to keep shields on while in use. The last point is neat as it's insurance against getting an unlucky rocket or EMP blast to the face while in transit, which can otherwise be fatal. When player controlled, I'd say that the Manta(M) handles much better than the regular Manta simply due to that.
The PD is kind of for missile and fighter defense, but it's also for making the most out of targets of opportunity: Stranded frigates/Destroyers. Burn directly into them, overwhelm their shields with ballistic fire, de-teeth them with the ion cannons, and finish with the Crossbows. If the Crossbows hit, a frigate is probably dead and a DD (or most cruisers) is seriously hurting, and is vulnerable to follow-ups from others in the fleet due to disabled systems by the ion cannon.
If no such target of opportunity currently exists, though, you can still harass near-peer Destroyers with Railguns + Ion Cannons + Bombers without charging into the opponent's battle lines.
The Manta(M) still sucks at doing much to heavy DDs and higher, at least not alone. There are some exceptions though: I've been able to take out Disassemble Reassemble's Barricade combat freighter which is cruiser-sized. Granted it's a combat freighter, but I still think it's not bad considering the Barricade has 2 fighter slots and the Manta(M) has only 4 or 5 small hardpoints available at any one time outside of point blank range.
I definitely wouldn't deploy it first in a huge battle dominated by capital ships, but it's definitely going to see use in pursuit settings. It's my favorite small ship to come out of this mod.