Sorry, but I'm having a hard time seeing the downside here. The tale of a plucky band of heroes driving the Evil Empire out of their once peaceful land is a classic because it happens to be realistic. A smaller, organized group focusing on one thing does have an advantage over a larger group with a wide variety of interests, and often times the smaller group succeeds not because THEY hurt the larger group, but because dealing with the smaller group is too expensive or leaves them vulnerable in other, more critical, areas. Yes, it is annoying for the Evil Empire, to be thwarted like that, but they wouldn't be an Evil Empire if they stayed home and knitted.
I can also see things from the player faction's point of view. Here you are, a small group of players who have banded together to free your home from the local superpower, you've finally succeeded, and then along comes another superpower who claims that your system is theirs, your chosen faction is costing them time, money, and effort, so you've got to go. From such things, depth of gameplay is made.
And while I do get your complaint about player groups being "invisible," that is the result of a decision Frontier Developments made before the Kickstarter, and I have no desire to discuss that decision once again.
I can also see things from the player faction's point of view. Here you are, a small group of players who have banded together to free your home from the local superpower, you've finally succeeded, and then along comes another superpower who claims that your system is theirs, your chosen faction is costing them time, money, and effort, so you've got to go. From such things, depth of gameplay is made.
And while I do get your complaint about player groups being "invisible," that is the result of a decision Frontier Developments made before the Kickstarter, and I have no desire to discuss that decision once again.