But Knowledge Raging would be such fun
Anyway, what I'm thinking is that the humans would have to build up some sort of research network, so in order to actually get knowledge from one you'd have to have, say, 4 of these special stations in the galaxy, and they'd have to be at least 2 hops apart from each other. That's a couple new mechanics but I don't think terribly difficult considering that command stations already have special placement-eligibility logic. Also, I think the knowledge gather rate would be 1/s, so if you wanted the k fast you'd have to do something in addition to that. Probably a moderate wave multiplier on the stations too, but nothing precipitous.
The goal behind the minimum-station-count requirement being to make sure you can't do it super-early game; the numbers being subject to change of course.
Anyway, thoughts? I'm sure someone can shoot it full of holes
Of the ideas I've seen, I like this one best because it keeps early game K-raiding the same, when it is important and a challenge.
I would suggest a more stations per higher mark system requirement (Mk I 3 stations, Mk II 5 stations, Mk III 7 stations, tweak as needed) so that the knowledge income is spread out over the game rather then you reach a magic number of stations and get all the knowledge at once.
A second and separate idea is a "knowledge cache" structure that is tractor-beamable and spawns next to the command stations (including your own on game start). Your science ships have to be within X (I'm thinking 25000 or so) distance of the cache to gather knowledge, or you can tractor the cache back to one of your planets and get the knowledge that way. This would be a 'raid' in that you are getting in, grabbing the cache and getting out, while still allowing the sit there and gather method without the 'transport to the edge of the map' method. Would be captured on planet ownership change so you can get the knowledge out after taking a planet. You would have to add a tractor beam to science ships and change knowledge to a "per cache" basis rather then a "per-system" basis though, so I'm not sure this is actually viable.
The last idea is that while Science ships can gather knowledge in a system without a friendly command station, they must return to a friendly system to actually pass that knowledge up the chain and make it useful. They would lose all knowledge gained from a hostile system if they enter a transport. This would allow you to still transport science ships past mines or when you are bypassing a system you haven't neutered, but prevents the 'transport to system edge' method as science ships would have to leave the system under their own power for the knowledge gained to be usable.
At the end of the day though, I'll get behind any change that:
a) nerfs the 'transport to edge of map'. (I see this as being overpowered or at least unintended.)
b) keeps early game K-raids similar as they are very important in the early game and worth your direct attention
c) changes how K-raids work later in the game. Your main fleet doesn't even notice most Mk III worlds by this point, so K-raiding as it currently stands is just time-consuming.
My $0.02
D.