I would love it to have a part where you can get your gun to a techmarine and he replaces parts or adds to it to make it more efficient.

I think upgrades are planned addition to the game while you're on your ship, like the planetside 2 attachment system I believe but with abit of an RPG twist to it.

The WH40K RPGs (Dark Heresy, Deathwatch, Only War, etc) have a large number of attachments for ranged weapons, like laser sights, shot selectors to choose between ammo types, telescopic sights, motion predictors, and even gear with some suitably 40k-themed names like "preysense sights".
I think we'd undoubtedly see some of these attachments in EC.


More on topic, different patterns of weapons would not be out of place in a game like this. I would expect that they'd have minor improvements in some areas with a commensurate trade-off in other areas.. like a slight increase in accuracy, at the expense of a slight decrease in damage. Or a slightly larger magazine, but with a slightly slower reload.
Games like Planetside and Blacklight have such ideas in place, and the 40k concept of different "patterns" of wargear give room for a background-friendly way of putting it into EC.

In addition, there's the concept of rare, artisan-built "Master-Crafted" weapons in Warhammer 40,000 that would be superior to their more mundane counterparts, though I'm not sure how this would fit into EC.


Meanwhile, to quote Starlight Berserker:
"It shouldn't get as stupid as that Stalker-pattern Bolter out of Spess Muhreen but a tad of variety should be there for the Beakies to fine-tune their builds."
Allow me to correct you.
"It shouldn't get as stupid as that Stalker-pattern Bolter out of Codex: Space Marines, 5th and 6th editions."
If you've not heard of Sergeant Telion, the wikis should have a page on him.

Aside of that, I agree wholeheartedly with having some variety to let players tune their armaments to their preference