Rework Mystery of the Trinity to be less dead space. I haven't gone through with a stopwatch to figure out how much of that mission is following your wingman from waypoint to waypoint with no dialogue or combat, but it's a lot. Also maybe unlock the ****ty armament you get stuck with. **** Rockeyes.
As I recall, Mystery of the Trinity doesn't replay well, but I remember a very positive first impression many years ago. It feels lonely, in a somewhat tense and atmospheric way, and you're seeing the nebula for the first time.
*watches QuantumDelta's let's play*
There's a lot of sitting around while NPCs talk, but only 2 30-second stretches of complete dead air.
Rockeyes would be fine (as a weapon for just the first few missions) if two things were different:
1. If tempests weren't so amazing. Sure the Rockeye has better range and isn't a dumbfire rocket, but the DPS and cargo size can't be beat.
2. If later in the game you got a much better heat-seeker. The Rockeye is a little tricky to learn to use effectively, and there's just no payout for learning to use them, because you get much better weapons so soon.
I say fine, because in at least the first three missions it's perfectly alright to fight entirely with Subachs and just ignore missiles entirely. Learning to use heatseekers or dumbfire missiles is just a bonus. But then in mission 4 you get the intuitive and effective harpoons and it's like... why dogfight with anything else?
However, your specific point about Mystery of the Trinity is fair - you just got new weapons in the previous mission and now you can't use them? I figure they thought the Dragons weren't scary enough if you had harpoons, or something like that.