Two thumbs up to Vipervenom for starting a new discussion to seriously talk about this mod. The Mass Effect universe is too interesting and developed in story for Sins to ignore. I'm no modder but as a Mass Effect fan and someone who would play this kind of a mod, I'd also like to contribute my thoughts if no one objects to hearing them.
K, well first off, on instinct I really like the idea of converting wormholes into a mass relay network. It's the most logical option in order to include them. However, I might suggest making a research requirement for you to be able to activate them once they're found. Might make expansion a bit more of a challenge and slow things down nicely. And as for star travel, I don't know if I would take it out completely. The point to the mass relays is that when you go through them, you're not limited to that single star system, but to the entire local star cluster. However, I don't know if it's possible to implement any kind of system like that in the game, so if that can't happen then oh well.
Second, I liked Yanxa's suggestion as to starting with only two factions. For a beta or a first release it would be easiest for a modding team to just create a Citadel faction and then an opposing faction, whatever the team decides that to be, Geth, mercs, etc.. We've seen several different ships throughout the two games so far, but barely enough to constitute entire individual fleets.
Third, the ships and factions. The singlemost important element to the success of the mod. The Alliance Navy is the easiest - or the least difficult, that is to say - to model ships for, because we have pictures for three of their ships and codex details for how the other components of the fleet operate. We have the first Normandy to have a basis for small frigates, the Alliance cruiser from the Battle of the Citadel, and there's also a picture of a fighter on the "Starships" main page on the Mass Effect Wiki. From these three we see that the common element to Alliance ships is their wings and engines, running parallel to the main shaft of the ship and hanging at an angle. Also, on the carrier we see two main guns projecting out of the front of the ship. Also, from codex details we know that dreadnoughts have a similar cannon running almost as long as the ship itself, so we might assume that this as another common detail to powerful ships.
It's the other Council races which would probably make up the main factions that present a problem to a modding team. For the salarians we have absolutely nothing to go off of. With the Asari there's the famous Destiny Ascension, but we don't know how this dreadnought relates to the rest of their fleet. The same goes for the Turians, where at least we have a common cruiser from screenshots. All you can do is focus on the prominent elements of those two ships, and try to apply them to other ship types. With the Asari, you have that abstract four-point cross design and a hollow middle. Oy vey, all I can say is good luck with the asari, that's hard to work with. For the Turians, at least they're a bit more straight to the point in style. Long broad shaft opposed to the roundness of the Normandy or the narrow boxiness of the Alliance cruiser. And their wings are more at an angle like a V shape, not parallel like Alliance ships. Might be easier to apply to different ships.
With the release of Mass Effect 2, we also got a new look at the Quarian Migrant Fleet. There are plenty of views of some of their ships, and since we have that, I don't think they should be left out of the mod. I don't know if they can be included in the mod, but I think it would be a waste of starships to ignore them.
The geth have their dropships, which have been labeled as frigate-class. Also in Mass Effect 2 we saw a geth space station. I suggest look at those two and compare for ideas.
I really wish that there were images of krogran spaceships, I don't believe they should be left out of the mod, but maybe they'd be better for a role as pirates or something.
And remember you even have a new model for trade ships by replacing them with Kowloon-class freighters.
