OK, but before you do that, let me explain how the CM universe works. Every sector has a difficulty level (1 - 10). The strength of the alien fleet is based on that number. For simplicity you can assume the range to be from 10 - 100 points. Likewise the player has fleets in nearby sectors that also range from 1 - 10 (10 - 100 points), which are calculated in an attack as 50% of the closest sectors and 25% of the sectors that are 2 jumps away. Example: You could have 2 directly adjacent sectors, each having a fleet strength of 8 and one that is further away with strength 10. The attack fleet would have an overall strength of 0.5 x 8 + 0.5 x 8 + 0.25 x 10 = 10.5 or 105 points. Assuming that the sector you attack has difficulty 8 or 80 points, the ratio would be 105 : 80. What's still missing is how to map the 105 points of the EDF to ships, i.e. what kind of ships would the player receive in actual battle for the 105 points? Same question applies to the aliens in terms of masterminds and factories. The aliens are actually a bit more complicated, since they use masterminds during attacks on your sectors and factories when they are being attacked by you. Masterminds only produce one ship at a time, while factories can mass produce. On the other hand, masterminds can escape while stations remain stationary. Factories have much more armor than masterminds. Yeah, this is where it gets really complicated and finding the right amount of balance will be really, really hard.
Let's begin with the aliens when in defense. There are two types of factories. Light & heavy ones. Light factories produce normal carriers, fighters and corvettes. Heavy factories produce destroyers, battlecruisers and drone carriers. When reactors are added to the factories the production rate is increased. When one reactor is added, it is doubled and when two reactors are added, then it is tripled.
Light factory production time (no reactors):
Light Fighter: 67.5s
Heavy Fighter: 72s
Light Carrier: 76.5s
Heavy Carrier: 81s
Light Corvette: 85.5s
Heavy Corvette: 90s
Heavy factory production time (no reactors):
Light Destroyer: 144s
Heavy Destroyer: 153s
Drone Carrier: 162s
Light Battlecruiser: 171s
Heavy Battlecruiser: 180s
Here is what I've done so far, given the difficulty of a sector:
Aliens in defense:
1 - 2 light factories (1 reactor each).
2 - 2 light factories (2 reactors each).
3 - 2 light factories (1 reactor each), 2 light factories (2 reactors each).
4 - 4 light factories (2 reactor each).
5 - 2 heavy factories (1 reactor each), 2 light factories (1 reactor each).
6 - 1 heavy factory (2 reactors), 1 heavy factory (1 reactor), 2 light factories (1 reactor each).
7 - 1 heavy factory (2 reactors), 1 heavy factory (1 reactor), 1 light factory (2 reactors), 1 light factory (1 reactor).
8 - 1 heavy factory (2 reactors), 2 heavy factories (1 reactor each), 1 light factory (2 reactors).
9 - 2 heavy factories (2 reactor each), 1 heavy factory (1 reactors), 1 light factory (2 reactors).
10 - 3 heavy factories (2 reactor each), 1 light factory (2 reactors).
Aliens in offense (all masterminds):
1 - 1 x corvette, 1 x carrier, 1 x fighter
2 - 2 x corvette, 2 x carrier, 2 x fighter
3 - 1 x battlecruiser, 1 x destroyer, 1 x drone carrier, 1 x corvette, 1 x carrier, 1 x fighter
4 - 1 x battlecruiser, 1 x destroyer, 1 x drone carrier, 2 x corvette, 2 x carrier, 2 x fighter
5 - 2 x battlecruiser, 2 x destroyer, 1 x drone carrier, 1 x corvette, 1 x carrier, 1 x fighter
6 - 2 x battlecruiser, 2 x destroyer, 1 x drone carrier, 2 x corvette, 2 x carrier, 2 x fighter
7 - 3 x battlecruiser, 3 x destroyer, 1 x drone carrier, 1 x corvette, 1 x carrier, 1 x fighter
8 - 3 x battlecruiser, 3 x destroyer, 1 x drone carrier, 2 x corvette, 2 x carrier, 2 x fighter
9 - 4 x battlecruiser, 3 x destroyer, 1 x drone carrier, 2 x corvette, 1 x carrier, 2 x fighter
10 - 5 x battlecruiser, 3 x destroyer, 1 x drone carrier, 2 x corvette, 1 x carrier, 2 x fighter
Now these are all numbers and the only way to make sure it's balanced, would be to try it out. Concerning what the EDF will receive in terms of gear / fleet size, I have no idea yet. Spent most of the time programming all that stuff in and fighting the most difficult levels using the main fleet.
The next step will be to do the same for EDF, but it will be easier, since there is no difference between defense and offense. Basically what we need is something like this:
1 - 2 Heavy centaurs, 1 Laser Centaur, ...
...
5 - 1 Cerberus, 1 Hydra...
...
15 - ...
you get the idea.
The maximum should be level 15 in my opinion, so even if the surrounding attack fleets give you more attack points, you will get a level 15 attack fleet. In defense you will of course have a maximum of level 10 (the local fleet).
A pretty long post, but I hope it clarified the problems we are facing right now. Any input would be greatly appreciated.

@joe
Yes, in defense you have the HQ, which has 1000000km of radar range, so nothing can hide, not even masterminds.
