Something I've always liked doing in the game is maintaining a faction-specific fleet. I find it interesting to play the faction with its notable strengths and weaknesses without using other faction ships to shore up those weaknesses. While it's an interesting thing to mix technology, I feel there should be a drawback to picking and choosing the best of each suite of technology. Enter: Fleet Coherence.
A fleet statistic, similar to Logistics Rating or CR, that determines how consistent the technology is in your fleet. This is a measure of interchangeable parts, compatible interfaces and computer technology, and similarity between ships. It would likely have an impact on one or both of the above, as well as increase supply cost, as you need to make use of your supply reserves instead of being able to copy and/or re-use parts from other ships to repair them.
So if your fleet consists of a hodgepodge of heterogenous ships, your Fleet Coherence would be very low. But if you were to stick to only low-tech/Hegemony ships, your Fleet Coherence would be high and you'd gain slight bonuses. The average level would be somewhere in the middle, and would give no or negligible penalties; you could have a few ships of a different technology without it being too big a deal, unless they're Cruisers or heavier.
This would probably also apply to ships using weapons (and possibly even hullmods) of other factions or technology sets. Fleet Coherence could also be modified by the Technology tree (not that I want to make that tree even more useful than it already is, because it seems to be a little more powerful than it ought to be), to reduce its impact; reflecting your character's intimacy with a variety of technology and capability of understanding it and adapting it to other brands of technology.
This is likely going to be controversial, but I feel this would allow for more unique balancing between factions. It also opens the door for awesome stuff with mods; technology can be assigned in terms of keywords that both the core game and mods could make use of. It could use something like a tier system (where fleet coherence is retained partially for 1-2 steps away from your tier) or it could just be something like "Hegemony tech" or "Corporate tech." You could even have more exclusive keywords like "Alien tech" that would cripple fleet coherence, at least for that individual ship, allowing modders to make certain ships unusable if they so choose (Uomoz's aliens come to mind here, as might the Zorg).
I personally like the idea of making this quite a fleshed out system, at least under the hood; you could have overall technology sophistication, which describes how advanced the technology is, and then you can have keywords to describe who, if any, the tech is specific to. For instance, factions like Lotus Pirates or Junk Pirates largely use cannibalized and adapted vanilla technology, so their tech wouldn't really be specific; this means their effect on Fleet Coherence isn't necessarily that big (or it could be the other way around). Factions like Neutrino Corp might have some things in common with factions like Tri-tachyon, meaning they could be largely compatible with each other, whereas the Antediluvians and Nomads have utterly alien technology compared to the rest of the sector (even though Antediluvians are very low tech and Nomads are high tech).
This would result in fleets that might contain both Hegemony and Ifed tech, as they're similar enough not to harm Fleet Coherence too much. But if you use fast and efficient high-tech frigates and fighters with defensible and rock-solid low-tech cap ships and cruisers, you'll pay more for that versatility.
I think it would add depth to the game in an intuitive way that wouldn't step on too many toes. As long as it's not done in an excessive way, you could still have your independent mercenary fleet composed of any number of ships you want! There'll be a drawback to it though, giving you a reason to stick to a certain line of technology.
Discuss away!