So the way I read this, the two new formations that are specialist-only are the paired Covenant CCS battlecruiser and the paired UNSC
Marathon elements. Other than aesthetics, I think these new formations are only going to help the Covenant, and here's why:
Battlegroups cannot exceed a build rating (BR) of 6. Battlegroups must also contain at least one capital and one non-capital element. An unsupported Covenant CCS has a BR of 3 and is a capital-class ship, meaning it is impossible to run two CCS battlecruisers in the same element (as you would have no BR to add in any non-capital elements). Now, this specialist element of two CCS battlecruisers will be a battlegroup unto itself, because it's BR is 8--no room to add anything else. This will allow the Covenant player to run two CCSs in one battlegroup, although they'll have no supporting ships in their battlegroup. This means that battlegroup will lose one weapon system; CCS battlecruisers carry a plasma lance and a plasma cannon array, but no plasma torpedos (these are provided by the SDV heavy corvettes). But the firepower of two combined cruisers might make up for that; the plasma lances are 9 dice apiece, so that's 18 dice at Firepower Rating 3 at long range (18-32") and 18 dice at Firepower Rating 5 at short range (0-18"). That's enough to potentially kill even a supported
Marathon at long range, if you don't roll dice like I do.
UNSC players can already run two
Marathon heavy cruisers in one battlegroup, as long as they are unsupported; their BR is 2. UNSC frigates in trident formation have a BR of 1, so UNSC players can already run two unsupported
Marathon elements plus two elements of frigates in the same battlegroup (and I have already seen the combined MAC fire from one of those battlegroups eliminate a fresh CCS in one salvo at long range). Like the new paired CCS element, this paired
Marathon element will be a battlegroup unto itself due to it's BR. So I don't see this helping out the UNSC player that much.
But...I haven't played with these formations yet, so my opinion may change over time.
Just my $0.02.