Good evening all!
In SCII, customization of the Precursor ship was a major factor in the success, or failure, of the player. It is possible to win the game without utilizing any of the Melnorme ship upgrades; but it does add a degree of difficulty.
The Mass Effect series did a wonderful job lifting ideas directly from SCII (ship customization, evil galaxy-threatening giant squid, blue space babe love interest, floating fish/jellyfish who's speech doesn't quite make sense...the list is long, but distinguished), and customization of the ship had a significant effect on the overall narrative. Personally, I would like to see ship upgrades expanded in scope beyond those contained in SCII and/or Mass Effect, so that different play styles can be tried based on the "build" of the player ship.
Some upgrades should be universally useful, such as speed/turning rate enhancements or fuel tanks. Others should be for defense-minded players, like the point defense laser system, armor upgrades, or a shield system. For aggressive players, traditional weaponry upgrades, aim upgrades, and a secondary fire mode.
For tactically minded players, upgrades that allows the player ship to take on a special ability based on the technology of peaceful races or ships within the fleet would add another layer of choice to combat. These abilities would have to be carefully balanced, so as to not mitigate each race's existing special weapon, but would give the player ship a unique feature that is identifiable as species-like. Also, in the interest of balance, make it a one-off, usable only once per hyper-melee, or give the ability a significant cool down. Also, not all species abilities necessarily need to relate to combat; they could be passive, and aid in exploration and/or interaction with other species. Off the top of my head, the following are examples that would make racial sense, with a few specifics:
Psionic Races: Syreen, Pkunk, Dynarri, Taalo (immune to psi), Utwig, Exquivan, Clairconticlair, (immune to psi), Chenjesu (how else do they communicate?) - Expanded/different dialogue options (adventure/RPG mode).
Mechanically Inclined Races: Mrrmhrrm, Daktaklakpak, Doog - Enhanced mineral resource collection, reduced repair cost/time (adventure/RPG mode).
Biologically Inclined Races: Umgah, Supox, Mycon, Androsynth, Xchgagger, Lk - Enhanced biological resource collection, enhanced crew healing (adventure/RPG mode).
Economically Inclined Races: Druuge, Melnorme, Ploxis - Cost reduction at stores (adventure/RPG mode).
Militarily Inclined Races: Ur-Quan, K'Tang, Illwrath, Vux, Harika-Yorn, Yheat, Shofixti, Earthlings, Viro-ingo
Other-Space Races: Arilou, Orz, Owa, Slylandro - ...I've got nothing. Ideas?