Disappointed ...

I am curious why people want the Trademark ship in this game? It is basically a Harbinger with an extra gun port and heavier armor and shields. While I love Trademark in Harbinger, this is a totally different game.
Has anyone actually had success at higher difficulty levels using the multi-bay ships such as Harbinger and the CloudWhatever? Or even the Overseer?

I personally have found ships with multiple bays to be completely worthless, in particular the larger and more expensive ones. Only 1 bay is needed for marines of course. By the time you can afford stuff like Harbinger or Trademark, you would already be at max # of bays by going with a station-based approach.

I have found very little advantage in having fighters stay local (Defensive), vs letting them roam when using a 12 bay strategy.
If I am not going with 25 pilots, then I can use the slots for say Plasma Bombers or Laser Drones, but in most cases I'd rather just have an extra gun slot.

One thing you will discover is that strategies which are great on Easy, don't work so good later on. :-) I had quite a bit of adapting to do during my playtime. Beating Legend was no joke!

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As for your suggestions,

Queue for research sounds like a great idea! And easy to implement hopefully.

Ability to use XP to buy "Mastery" for each tech type to have the first tier auto-unlocked could be a good way to add game progression.

Would be nice to Perma-Save ship designs although I can see that as a problem with foreign ships. (stuff u captured and saved).
Adding multiple guns of 1 type at once seems easy and worthwhile.

I would not mind seeing repair modified a bit. Remember however that your battlestation repairs for FREE, although slowly. If repairs were limited to friendly nodes (which makes sense), I'd expect the cost to decrease significantly.