My Suggestions

1. I know that you are no longer going to have the Asgard beam weapons on every BC-304 but what about shields? Why not allow the user to research a shield upgrade and railgun upgrade as they progress. As seen in Atlantis series the new railgun type is blue instead of the yellow coloured and when the Asgard give Earth the knowledge base before they push up dasies the get the new shield technology. A nice addition would be the plasma based weapon that Felger works on in SG1 "Avenger". It would be nice to have something other than missiles and railguns for Earth ships.

List of things you could research:

Blue railguns
The latest Asgard shields
Lastest Asgard sensors which would increase your ships field of view/weapon range
Felgers plasma weapon

2. More realistic Wraith projectile damage and particle effect size. In the series the Wraith weapons cover a large surface area of Earth ships when they impact.

3. Ancient ships have drone swarms as a special abaility, instead of just a line of drones hitting the target they would cut in and out of the enemy ships.

4. Ships have sensor arrays which allow ships to target the enemy. If they are destroyed then their fire is less accurate.

5. ZPM's can be attached to a ship each and deplete over time during battle.

6. Earth uber ship with giant ray gun.

1. Railguns:

First Railguns: The yellow short range weapons of the prometheus
Second Railguns: The blue Railguns seen in "Siege Part II". Never used on a ship in the series. (In our mod all x-303er use this railguns)
Third Railguns: The yellow high range weapons from the Deadalus and all other Bc-304. Our Bc-304 in the game will use them from beginning. Maybe in 1 GC you can build X-303 with the first Railguns.

suggestion 3 and 4 is rly good ones, but they're not possible due to the Game setup. Keep up giving good suggestions, all of them wont be turned down ( hopefully) unless they're not all like suggestions 6 ^^