I would like to see campaign writers break the mould here and have the player retain learned research in subsequent chapters. It has never made any sense to me that a player loses everything they have learned when moving on.
Yes - I personally would
hate to have my empire comprised
entirely of amnesiacs

Personally I don't care about a campaign in 4X game, not only because they usually don't need one, but also because I rarely see one that is done in a way that I can agree with.
I share your opinions on GalCiv2 (I don't have the expansions), but I believe the general consensus (correct me if I'm wrong) is that this is more of an RTS than 4x (though I personally believe the 4x elements that do exist make the game so much better - I'm not sure if this is also a general consensus, but meh), and therefore warrants the campaign more. Considering the fantastic context of Homeworld and what its makers made of its campaign, perhaps something similar could be done in this case, especially with the Vasari pursuer. This appears to be the attitude of the expansion and its campaign.