I'm not sure if there is a way in mods to prevent boarding operations from taking place. It's possible to capture AI or Alien ships.
The 100 deployment points makes it a little difficult to field, at least.
So having played each of the 4 main factions to the endgame states (Engame for me means I can beat any fleet in the game without losses, with the possible exception of a 3+ Harpoon Wing Marauder Fleet), the ISA now feels easily the strongest in terms of hulls, since the Indiana-C can form the backbone of any fleet, and the Illinois is the best ship in the game when used by a competent player. The F-171 is the most survivable fighter in the game, although it's a little lacking in speed and firepower. All of the fighter wings are fairly good. ISA weapons are lacking in good small slots, but the player can solve that problem by buying elsewhere.
The UIN have the best cruiser hulls and a few specific powerful weapons, such as the Particle Beam and the 60 pound dual siege cannon. The biggest problem they have is a lack of decent HE ballistic or energy weapons. They have a lot of different Kinetic weapons, but with the exception of the 60 pound dual siege cannon and the terminator autocannon, as well as some missile systems, they lack solid HE damage in their fleets. They also have very specialized Frigates.
XLE have some great dueling/solo hulls, as they are maneuverable and the AI understands how to handle them reasonably well. It's really difficult to mount anything but Beamers in the energy weapon slots due to the flux weapons. However, Beamers of all sizes are extremely flux efficient, and I consider them to be among the best weapons in their class. They also offer advanced 42mm autocannon/flak weapons, which are good and flux efficient. Magna Cannons/Heavy Magna Cannons are also good HE weapons.
The RSF has some good weapons but bad hulls.
My one gripe with the Germany is that it doesn't feel much like a broadside ship. You generally want to face the enemy head on, where your forward 4x Small Ballistic mounts can fire, as well as you 2x Large Ballistic mounts. Combined with the support of 4x Small Missile mounts able to hold rockets or torpedoes, and 8x small missile mounts, as well as the 1x Large Missile mount, there is a lot of firepower in the front. I'd much rather see 8x small missile mounts in the front, and have all the mounts along the side be small ballistic slots. That way the front of the ship can still mount a lot of strike weapons, but are used as a finishing blow, somewhat like the Conquest in vanilla.
One small issue I have with the larger RSF ships is that their Large Ballistic mounts that point sideways take forever to face forward. This means that against an AI Novagrad, you get at least 5 seconds of firing on it before it starts to unload its 500 Kinetic DPS from the 2x Quad 50mm Autocannons. Don't know if there's anything in the API for it.
I really think that the FFS have nailed the 'raider' style with their ships and combat doctrine. They mount a lot of Kinetic weapons and high DPS/high flux energy or EMP weapons, and then use missiles to inflict major damage when the shields go down. They are very nasty to face in an unfair fight. By comparison, the Widows tend to get into a brawl with the lower DPS energy weapons, although they have the Barracudas for when shields go down.
I would somewhat like to see Marauder ships have their weapons loadout randomly generated, since they would scavenge whatever ISA/RSF stuff they could find.