Yeah, I get what you mean about missile hit rates.
I've put terminal guidance on, which makes it about 16% per pass, plus 4-part warheads, which gives 4 chances at that 16% per missile on the "cheap" 1.75 AMM. Figure on average that gives me a rough 50% per missile. Then on the bigger, longer range S3 AMM I've added retargeting on top of those features with enough range they should get 8-10 kicks at the can with 4 sub-munitions. Both also have ECCM to help reduce the effect of decoys.
Your AMMs get 1 try at 10% per pass, mine get 4 at 16%. That makes a major difference in effect. Getting the submunitions costs, of course, the "cheap" missiles only get 1 try, and the "good" ones are 50% larger than the ones you're using. However, I'll take 50% larger for 5x more effective. The cheaper ones are for the poor sods I keep meeting with far less than top tech.
If I knew I was going to be facing "real" top-tech, well-designed missiles, I'd load nothing but S3 AMM 4x15 RETs.
Also, while your missiles may have longer range, you don't have the MCR on your sensors to use it. See below about the sensors.
Are they perfect? Nope. Are they better than 10%? Yep.
It's worth noting, though, this isn't primarily a defense vessel. The defensive systems are there to add a little weight to a fleet, or to be capable of killing those random pirates that sometimes just show up out of nowhere. This definitely isn't a primary combatant

See Requirements 3 and 5, and the use of "modicum".
Speedwise, I've run into 100,000 ton ships doing 35,000 kps, so my direct combatants have a minimum speed of 40,000 kps but are generally a little faster. You had no way of knowing what "keep up with major fleet elements" entailed, though.
However, before all that, item 1 in the requirement was a MASSIVE sensor fit. Specifically stated was "size 50 sensors".
This is the ship whose primary job is to see hostiles at the maximum range possible. MCR on a 50 HS max tech sensor is 41.7, and the R100 sensor can see targets at a little over 2 billion kilometers. The R10 sensor covers fighters and FACs. I was tempted to do an R500 sensor just for giggles, but his thing was already getting ridiculously expensive and the R100 seems like enough.
Plus a flag bridge, (Requirement 2) this IS a flagship. Also passive defenses (Requirement 4, shielding) that won't fold because half a dozen missiles made it through, because anything that radiates as hard as this thing does is GOING to attract fire, and the layered defenses of the fleet may not stop everything.
I guess what I'm saying is you're asking me to rethink my doctrines about a completely different design issue
