So, I've generally avoided compilation mods - had some bad experiences with an early, totally unbalanced, everything-and-the-kitchen-sink type mod. But, actually started playing with yours a couple days ago, and it seems overall pretty good.
So, I figured I'd share some of my experiences with you.
Started off Supremacy / Shadowyards, since I rather like their ships. Found their missiles to be all but useless - unless the target was overloaded, they just get shot down. But they've got some pretty good energy weapons, so I just swapped to those instead.
Got a lucky early fight - took a Gedune cruiser down to 5% before it retreated... and then it surrendered, hull mods intact. So I stripped off what was left of its original armament, mounted three CEPC turrets and two heavy blasters, threw everything else into vents & capacitors & hullmods. Maneuvers like a destroyer, hits like a heavy destroyer or light cruiser (heavy blasters being no joke when you can actually support the flux generation), and - thanks to three large weapons worth of ordnance points I'm not spending on guns - is about as durable as they get. Once I have higher tech skill (and more ordnance points), I may go back and add some autopulse lasers; early experiments show that the resulting firepower is rather ridiculous - but at least for now, I have to sacrifice too much of my durability to get there.
So, remainder of commentary is from the perspective of flying around in that one cruiser, with some level of save-scumming used mostly for "I have no idea what those ships can do; let's find out!"; I'll probably try hardcore mode soon, now that I've got some degree of feel for how the various factions function in combat.
Can't yet take event / boss fleets - they're too big, and my one cruiser would just get swarmed. Maybe later.
Hegemony & IFed: I haven't fought them much yet; could probably take an onslaught due to superior maneuverability, but I'm not sure what the upper end of the IFed line looks like. From what I've seen, though, these look pretty balanced.
Vanilla Pirates: they just can't compete, really; I'd suggest giving them a few new variants, and maybe making some of their fleets use Conquest battlecruisers. If you'd like, I can make some .variant files for their ships; that takes all of a few minutes. (Maybe, if you want to keep the normal pirates as they are, making a boss or event? I'd love to provide a "pirate fleet" using high end maxed-out-skills type variants...)
Junk Pirates: Haven't seen any large fleets from them; the smaller fleets seem pretty ordinary.
Gedune: Odd faction; their cruiser is an exceptionally strong hull, limited primarily by their choice of short-range or slow-moving HE weapons; I took one out in my starting frigate without too much trouble, by the simple tactic of dodging and taking any hits that got to me on shields. Haven't tried fighting larger fleets, though - I tend to pilot a solo ship, and would just get swarmed.
BRDY: Seems roughly balanced. Can fight some of their bigger fleets with capital ships, but it's a hard fight where I can't afford to make too many mistakes.
Neutrino: Very pretty. Very thematic. Very very annoying to fight. Not actually dangerous, mind you, just annoying - their reliance on fixed beam weapons means they can't really hurt me, but their essentially impervious shields make the battles long and tedious. Got into a fight with one of their uber-shield-drone capital ships, and eventually got tired of trying to take out the drone and just rammed the thing until it ran away. Should not have been able to do that - if it had mounted more than one or two non-beam weapons, maybe some antimatter blasters in the rows of small turrets along its sides...
Antediluvians: Feels like a joke faction, with their tiny short-range weapons talking about "sonic" effects in space, and their unshielded ships that go boom if you look at them funny. Except their fighters, oddly; those seem more durable than most of their frigates. Dangerous if you let them swarm you, but too slow to actually do so; only their fighters are fast enough to be a threat, and then only in large numbers. Might be more dangerous if I was flying a slower ship...
Thule: Also unshielded, but much more dangerous than the Antediluvians; the smaller Thule frigates, with their heavy maulers, aren't a threat to my well-shielded cruiser, but once they get big enough to also mount kinetic weaponry... Fighting Thule is very binary - either you can just mulch them without taking much damage, or they've got too much firepower and will mulch you instead.