At a wild guess they failed to make the barrage system work without armour protecting against mesons.
Without armour mesons are way too good, with armour (and screens etc) the mesons are not good enough.
That bays are the primary defence against fighters is another fail for the barrage system...
I guess their failure in this sense was in the design system, where Meson Bays are too easy to install (as their power requirements are too easy to achieve) and the low power of the Meson Screens against them.
See that a 10000 tons ship with level 6 Power Plant (that would ammount just 500 dtons) may well have up to 60 meson bays. Even if they are 60 x 50 ton such bays (so amounting 3000 dtons), they can be devastating (as shown above), be it against fighters or capital ships, and it would still have over 60% of its tonnage (even accounting for the PP fuel) for other things (spinal, Drives, crew quartiers, armore, etc..).
For what I've read, MgT2E includes the power needed for each mount, and I guess Mesons will need quite a lot of it, so probably fixing this (as it happened in CT and MT, where bays were also limited to 1/1000 tons).
As for the power of the Screens, IDK only if you have lots of them they are really useful, as a FC/5 software and skill 3 are enough to nullify 4 layers of them, and if you add the dice (5 for those small bays), even the 6 maximum screen layers are of little use (unless you use the Screens to Full order, that makes them more powerful).
Again, to compare it with CT or MT, the screens were there quite useful against Meson Bays...