Cluster 1: Abandoning perfectly good craft.
The Hercules MkII is a good functional replacement despite different classifications, but I prefer the Athena. Faster, even better gun placements, copious afterburner reserves.
The Valkyrie embodied speed and precision like no other craft and was a joy to fly. To put it in perspective, the speed advantage over a Perseus is considerable bigger than the speed advantage of the Perseus over an Erinyes.
Terrans spend a lot of time and effort to build a Harbinger-compatible heavy bomber with a Banshee turret. Vasudans... had a Harbinger-compatible heavy bomber with 2 Banshee turrets all along... and they retire it.
Cluster 2: Abandoning perfectly good weapons.
The Avenger was an excellent general purpose weapon. A slight bias towards hull damage but still better against shields than the Subach, accurate, efficient.
The Flail and Shield Breaker were excellent complements to the Avenger (which took care of the hull damage), being far more efficient than their successors. 4 Avengers + 2 Flails is an excellent combination, and one that I'd often prefer to anything available in Freespace 2.
The Prometheus R is a useless piece of junk, which is especially annoying when it's forced on you. Retaining the Avenger turret in the Medusa would have been nice. The Osiris, while never a good bomber, would at least remain a respectable gunship with 2 Prometheus turrets.
Helios bombs may be more destructive, but in most anti-destroyer engagements I'd rather have Harbingers because of the performance against subsystems.
Cluster 3: Introducing the strangest new designs
The Myrmidon is a flexible if a little awkward craft... it can fill any fighter role except the one it's built for (too clumsy for a space superiority fighter). The weapons placement is unforgivable on the Artemis, and the Boanerges
The Vasudans are badly in need of a light craft that isn't unreasonably fragile. The Ulysses was supposed to be a joined project and would have been a very useful addition to them. Calling the Serapis an 'Advanced Interceptor' is a joke: it's too slow and can't carry Trebuchets. I like the nimble little thing but again, not suited to its supposed role.