So I love the new breath of life this mod gives the game after you've finished the story and explored the whole vanilla sector. But I have an issue and although I realize this is part of the intention of the mod, well...within the first year the Hegemony "won" the game by allying with the Persean League. Which is strange given who they are naturally...but also that was going on while I'm still in the early game diapers of an independent fleet.
Kinda takes the wind out of your sails, you know? So I continue playing because I've already sunk a fair number of hours in at this point. And now whenever I find a nice world to put a pin in and save for later colonization the Heg/Per alliance colonizes the planet first.
On one hand it's exactly what they would do if they really were a space faring superpower. Makes it feel like you're really in an RTS of sorts where you really need to keep up with the competition. Which is great for some players. On the other it kind of punishes people like me who like to take their time and wait for the right time for them. I like to explore every nearby system before I set my eyes on a colony site. I like a lot of other things this mod does but that, to me, makes it not worth the trouble. Anyway, I'm rooting around in the config to disable invasions or colonization's or expeditions or whatever stops them from expanding like wildfire.
The other "issue" here is that Nex is really meant to be used in conjunction with at least a few faction mods, in order to expand the board a little and increase the number of players. If you just stick with the vanilla four factions, a result like this is possible due to random diplo rolls - it's unlikely, yes, because the Hege and League are initially disposed mildly negatively to one another (both in raw relation score and in diplo profile), but it is possible for the two to ally, given the right set of circumstances. Adding more players increases the complexity of the situation and makes for a larger area someone has to ally with or conquer in order to win, and prevents early win scenarios.
If you want a decent bit of variety without feeling too overwhelmed, I'd go with four or five faction mods to start with. Specifically, Volkov Industrial, Diable Avionics, ScalarTech, Kadur Remnant and Xhan Empire (which includes United Pamed). Diable and ScalarTech will tend to ally very early, ditto with Volkov and the Hege, and Pamed and TriTach usually end up buddies too, so that gives several of the major players a buddy and makes it a bit less likely the big players will pair off with each other; meanwhile, Kadur will put the screws on the Hege from the start (though will probably get wiped out without help) and Xhan sits at the edge of space being *** to everyone. :V They also add a ton of variety to the game, so that's another plus!
But yeah, no matter how you go about it, Nex is best played with some faction mods to spice the sector up. When it's just the initial four, you can get results like what you posted.