it would work fine, although it would put the races too much into a weapons category, taking your example the sophons would be stuck on energy weapons (which they currently are to some extend because sophon and vodyani heroes have unique talents that improve energy weapon damage).

personally i think we have enough ship custimzation options, i think the game needs more work in other parts first.

keep in mind that the dev team still wants to implement fighters/bombers (this was scheduled for release)

I'd actually prefer if Minor Factions can provide unique modules (not only weapons). That way any major faction could potentially make use of any unique module. So you don't have any major faction being locked only to a specific type of weapon.

Part of the strategy in ES2 is guessing what weapon type the enemy will pick and equipping your ships with the appropriate counter-measures. But if you know, for example, that Sophons/Cravers get unique laser/missiles then there's no unknown element. It would very quickly devolve into hard-coded rock-paper-scissors.

There are already some minor pushes toward certain types of technology due to hero skills and unique techs. Voydiani are nudged toward energy weapons, for instance.

I think unique weapons absolutely could work and I posted a similar idea in the ideas section. The key would be to have the weapons not primarily be damage dealers, but instead provide a benefit that could be exploited by a savvy enough fleet commander/designer. 

Examples I thought of:

Sophons: Insight Torpedoes - These special warheads cause minimal damage but disperse nanite sensors across the target ship's hull which relay structural weak points to the fleet. The information results in increased critical hits for all other weapon types for a brief window during combat

Vodyani: Leach Beams - These special beam weapons convert a portion of the damage done to enemy ships into repairs across the flotilla. (Would deal less damage as a consequence)

I am thinking about to make a mod on specific colonization order for factions. But I really don't have any time for modding. And I know nothing about ES2 xml, even it should be very close to EL.

I think others parts, technology and ships should be also more faction specifics.

Maybe some people could make a important work about that, because it's above all conceptual, and this part take a lot of time.

Only problem is some ideas could be not doable because get some idea is nice, but apply it in xml modding is another thing, and sometimes, there is things a modder can't do because the limitations. But most of the time, all the game already do should be doable. If there is an improvement giving +10 industry, so it should be easy to make a new one giving +15, or anything else.

A Excel Datasheet for examle, showing all new stuff for all factions.

This need a project chief, checking all, and making datasave. With googledoc, there could be a workspace where anybody can edit files.

I just trow some ideas about collaborative working about that..