I've spent about twenty hours this week playing games with all these three factions on. I wanted to see how they work together, and whether they combined to make the game fun or frustrating. I've played with them all at intensities of 6 and 8, in different games. What follows are my observations and suggestions about them. I played at 7.6 difficulty for each AI, and AIP in mid to late games was 100-150. I'm not sure how each faction is affected by those factors, but I include them nonetheless.
The short answer is: these are very fun to mix together. You should try it.
I think Marauders are in a very good spot right now. At intensity 6, they show up every half hour or so, or when I'm being overwhelmed by, or overwhelming, the AI. They are truly equal-opportunity bandits: they'll happily wipe out AI forces as long as I don't engage them, and just as happily turn on me once they're done. They never allowed me to rest for long, and forced me to have at least a light defense on all of my planets.
At intensity 8, it seems like the only thing that changed was the frequency of attacks. I had to deal with them on average every 15-20 minutes. They still came in small groups of 40 or less, and caused the same kind of havoc that they would have, had I set them to 4 or 6. The only change I would suggest is that they come in larger groups on higher intensities, although this may make it frustrating rather than fun.
Resistance Fighters are hard to evaluate at the different intensities, because I could not figure out what made them decide to show up. In one game at intensity 8, I think I saw about 15 total, while in another at intensity 6, at least 50 over the same amount of game time. They seem to be the most random of the three factions I tried out. I would really like to know more about how they decide to help you: is it completely random, or do they come when you are suffering heavy losses? Are they more likely to come when you are further away from your own territory?
The Roaming Enclaves I tried mostly at intensity 6, and don't have much experience with them at 8. These are a lot of fun to have in my games. The hostile ones came about as often as the Marauders, and sometimes both would show up within moments of each other. In the early game, I needed to keep a small fleet in reserve to defend against these, but near mid-game I had sufficient defenses on each planet to hold most attacks at bay.
The Friendly Enclaves are a great help offensively and defensively. By default, they tend to cluster on your homeworld and not do much unless something attacks it. By the time they respond to a threat on a bordering world, I've usually dealt with it already. If you use the chat commands to disallow that, they become much more effective at defense. In fact, the chat commands allow a great degree of flexibility in how you use that fleet. I would like to see those implemented into other friendly factions like Resistance Fighters.
The fleet can get impressively large, too. After 9 hours in one game, I had 36 Friendly Enclaves ready to defend my planets, assist my attacks, or act independently. I would like to see something similar happen with the Hostile Enclaves in order to balance this. I rarely saw more than one of them attack my planets, and never more than two. If they could be made to cluster into fleets like the Friendly Enclaves do, that would make for more interesting, and frightening, scenarios.
I'm continually impressed with how much depth there is to this game, and how much effort goes into supporting it.