It's simple. Group clusters of systems into a larger tech upgrade we can unlock. If we defeat the 5 (or whatever) clustered systems, we get a super tech. Make the super techs not require a slot. Perhaps theme all the techs around artillery, bots, vehicles, aircraft, orbital, or naval. You can use the misc techs as filler in between these clusters. This would not only help balance the game because now we get nice progression towards something powerful, but now we can use the tech we are unlocking to defeat the rest of the cluster. It's incredibly annoying getting advanced naval tech and being unable to do anything with it.
Interesting idea. "Combat", "Speed" and other buff techs might be best for this. This in turn could increase the droprate of core tech, like basic/complete air. Of course that would change how this mode is played significantly.