I think something has to be done with the "IMMA DEPLOIN' MAH PARAGON WALL" mentality.
Does there really? It's slow, it's expensive, it depends on finding all the rare drops, and it's boring. If players insist on spending all their efforts into going full Paragon, there's not much you can do to stop them.
On the other hand... getting a default 360 degree omni shield, high levels of armor, superb offense, excellent PD, low crew requirements, an ability that clears out soft flux and good fuel efficiency in an all-in-one super fortress is pretty powerful. A vanilla paragon has no clear weak points, and it doesn't need hull mods to cover for weak points. It's truly a beast.