Just my two penneth, but the ability to take allied ships exists in V2... The alliance fleets are the 'motley' option, you are literally describing what is already there.
The Terran alliance Idea someone had above - it's already there in the fleet design as natural allies!
I hate to be the negative guy, but changing the macro lore of the game in such a huge way, by shattering the Kurak and Zenian leagues so the component parts have an official reason to duke it out - it just seems a change for a changes sake - a bit arbitrary.
However, if they get rid of current factions just so they can insert some of the WWX factions into firestorm, I will genuinely be horrified.
Warcradle don't NEED to change the lore, just refine it!
That bit of grognardiness aside:
There are some fleets for me which COULD, easily be detached from the alliances without retconning or changing the story too much - Oroshan, Corsairs, Traders, Bakash, Veydreth, Tarakians, Xelocians, Pathogen (I would add the syndicate and the Omnidyne here too - but retain their current natural ally status to represent their roots, likewise the veydreth and bakash)- in my mind all of these could operate like the 'Minions' of privateer press's Hordes (Except pathogen, obviously!). These all seemed like allies of convenience who would have their own reasons for fighting for or against literally anyone and those reasons are already all in the current lore - For me Make these an 'everyone else' faction if you must step away from just 2 main combatants, but at it's heart that was what made firestorm different to every other space opera fleet game out there (OK, starwars Armada aside)
And If I hear one more 'we're thinking about this from the point of view of the retailers' I'll scream - If no-one buys this from the retailers, the merchants won't care that you're only offering them 20 SKUS to wang on their shelves... It's like me selling beer by telling punters how easy it is to rack, tap and vent. Anyone like beer here? Ever considered that a valid selection methodology for what to decide what to drink?... No! me either. It's how good the pump clip looks and how good the beer tastes.
Now that sounds pretty negative, And I know WC have their work cut out (They are never going to please everyone) but I'd rather say it and nothing come of it than bumble along hoping someone else does, and being disappointed with the end result.