I agree that the hullmods are just too good at the moment. I'm not sure if they need to be removed entirely, but the difference in speed and combat abilities when facing multiple opponents is stark. It is true that i put them on all of my frigates - I've even tried to not, but the survival difference is painful.
When you put engine hullmods on everything and it is optimal, might as well speed up everything and remove the hullmod. In effect, making Unstable Injector builtin, minus the extra damage. In this case, Augmented Engines would remain for the extra burn and (slight) combat speed.
I remember when both engine mods used to stack, and I put them both on as many ships as I could. Augmented Engines giving a bit more combat speed is probably a consolation prize after engine mods do not stack anymore.
As for too slow, I think ships are too slow without them. They are slow compared to other games. I thought big ships (playable via mods) in Transcendence were slow, until I came here. Transcendence makes its ships look fast compared to Starsector's. I often feel like pressing my keys harder in a vain attempt to make my ships go faster in Starsector. Then again, AI in Transcendence automatically leads shots. Here, leading requires either high CR and/or Gunnery Implants, and without it, some ships can circle-strafe enemies with ease like in Doom.
@ Linnis: I do not expect the player to kill the Sa-Matra or the King chess piece to win the game, but if victory by combat is possible, I expect the player to take over all of the enemy's assets and maybe destroy every last enemy unit.