Late game, I normally only use SO via Brawler (LP) since they're incredible for capturing / competing for points early on to get your whole fleet deployed. They can then hunt down frigates and fast destroyers on the flanks or in places they got separated from the main enemy fleet. They're an annoyance on the battle line for a non-SO fleet which is fine since Hardened Subsystems + Combat Endurance PPT doesn't last through a long fight anyway. They're ridiculously strong early game. I don't think Brawler (LP) being raised from 5 to 6 DP really changed much. In practice, it means I can't include Converted Hangar Sparks in a 2nd Onslaught. I don't really understand why the player is allowed to restore the Luddic Path d-mod.
I strongly disagree about SO not being strong late game, other than SO flagships in a non-SO fleet losing most of their power. It's certainly one dimensional and gets boring. It eliminates zero flux boost (including holding fire / dropping shields for it), active venting and anything other than rushing in and in some cases escaping before you run out of flux capacity. Since it takes so much of your OP and you need powerful weapons taking full advantage of all the dissipation, that gets rid of a huge part of what's involved in designing ships. Your ships get a lot of safety from powerful shields and speed despite the need for aggressive tactics. All your ships can escape from anything unless they do something remarkably stupid which you can largely prevent. Orders work better when the ships are so fast.
SO cruiser fleets are extremely good and work fine against late game content. It's a lot simpler to build these than other ships. Assault Chaingun is no good against high armor enemies and you need ships able to mount Heavy Blasters. Both Eagles and Auroras got massively buffed in 0.96, and they worked well before 0.96. Hardened Shields got a buff. Eagles were already faster on average than Eradicators and now gained 10 speed, which is a bit higher when combined with 100% combat readiness and Helmsmanship. Extended Shields gives full 360 shields when built-in, and you can't afford several non-built-in mods anyway. Auroras have base 0.6 efficiency and a hull mod they already needed (built-in front shields) now gives a tiny bit more. The ships need to be strong enough to approach late game enemies and take lots of fire with their shield holding up. Eagle's movement system is perfect for the AI. Aurora is perfect for quickly hunting down fast ships and take more punishment when wrapping things up with Full Assault via shield efficiency.
As a simple example: 4x Aurora, 6x Eagle for 240 DP. Officers in every cruiser (player + 10). 360 shields on all of them due to built-in Extended Shields for the Eagles and Brawlers. You really don't need Systems Expertise and it's best for ship systems with charges like the Odyssey anyway. There aren't really a lot of choices with how to build the ships. 2x Heavy Blaster for both Auroras and Eagles, 3x HMG for Eagles and 1x Pulse Laser + IR Pulse Lasers in the other slots is perfect against Ordos. Optionally a single front PD Laser for Auroras if you feel it's needed to make them act more reasonably against missiles. If there were high armor late game enemies, you could use 3x Heavy Blaster with some IR Pulse Lasers omitted.
For both Eagles and Auroras:
Aggressive Officer
Combat Endurance
Energy Weapon Mastery - Elite
Field Modulation - Elite
Helmsmanship
Ordnance Expertise
Target Analysis
Aurora:
2x Heavy Blaster
1x Pulse Laser
7x IR Pulse Laser
1x Capacitors
35x Vents
Built-in Hardened Shields
Built-in Shield Conversion - Front
Built-in Stabilized Shields
Hardened Subsystems
Safety Overrides
Eagle:
2x Heavy Blaster
1x Pulse Laser
3x Heavy Machine Gun
3x IR Pulse Laser
0x Capacitors
31x Vents
Built-in Extended Shields
Built-in Hardened Shields
Built-in Hardened Subsystems
Safety Overrides
This is ridiculously strong. There's not very much to figure out for the ship design. There's not nearly as much for the player to do with their flagship because the overall fleet is too strong and instead your main role is getting the AI ships to be aggressive enough. I get quickly bored with it because you're so extremely powerful through the entire game. You don't even need the Auroras, just the Eagles and Brawler (LP). Late game, I have so much more fun flying an Odyssey or Onslaught alongside long ranged ships focused on forming and holding a battle line (Eagles, Eradicators, Champions). Long range fleets don't need as much use of orders and there's no rush, so in that sense it's better, but the power of SO Aurora and SO Eagle is extreme. It is true that if you don't use orders, your fleet will struggle to do more than kiting and picking off enemies that are out of formation until PPT runs out. It's not a fleet that plays itself, at least without Reckless officers which is a lot less safe than orders.
It worked before, and it works significantly better in 0.96. I don't have an issue with it being strong. I have an issue with something strong being so boring to play. That's why I think it needs changes. I don't know exactly what, but there are good ideas people have presented such replacing always-on zero flux boost with more bonus speed and reducing the flux dissipation but allowing active venting. That would add back missing core game mechanics and the balance could be kept relatively similar, while giving the player more of an advantage over the AI flying the ships (helping to reduce power of an entirely SO fleet). I think it needs more change that that, but it would be a good start.