Well i thought about this whole thing as well and i came up with an idea that could work, however i than scrapped it since i thought it would be too difficult to balance properly and also too complicated. Despite that i will share it with you...who knows maybe something good will come of it.
The basic Idea is also that you get points for kernels, however not just one big pool, but 9 (1 Structure, 4 Small[indu,blue,yellow;green] and 4 medium).
You would then have a research tree with tiers. The higher the tier, the more points you have to invest to unlock the technology. This way, unlocking essential items like mining modules would take far less work than unlocking items that benefit groups like nexus modules or remote equipment. Furthermore any item could have various prerequisites to be unlocked.
Every technology is also tied to one of 4 groups (small, medium, structure or independent) and 6 subgroups (mentioned before blue yellow green indu structure and universal).
To unlock a technology you have to use your points. The group of the technology and the group of the points have to match(except for independent, they will have different prices for every group) so you can only unlock structure technologies with structure points etc. The subgroups work a bit different: If you want to unlock a "blue" technology but you have only "green" points, you can do so, but you will have to invest twice(or any other value) the number of points. Universal technologies can be unlocked with any subgroup(except for structure, they are separate).
Examples:
1.) LWF: Independant, Universal: Can be unlocked with any points except structure, has different prices for small and medium groups.
2.) Medium EM-Gun: Medium, Blue: Can be unlocked with medium blue points or medium yellow/green/indu points for a higher price.
3.) Medium armor plate: medium, universal: can be unlocked with any medium points.
If such a system is introduced existing knowledge bases could be "refunded" with the new prices in mind. This way also partly unlocked items would be converted into points. You would be able to instantly unlock everything you had unlocked before and possibly a bit more.
The system could also be extended with diminishing returns so that unlocking a technology from a tier makes all other technologies of this tier more expensive. The total costs to unlock everything would always be the same but the way getting there would be dictated by the current needs.
Another good point of such a system would be that it does still encourage trade of kernels while it also allows "single-players" to work towards unlocking just stuff that it is important for them.
So far my brainfart on that matter...