Maybe this too late to consider something like this, but remember in MOM when you could only get so many spells based of how many books you picked?
When we finally see some balance in the tech trees, perhaps the super rare techs and and the 'powering up' ones could only be available to you if you specialized in that specific tech?
Kind of like the Group of traits you can pick a specialty from, but to state your preference for knowledge.
Say I chose magic, then all the magic tech would be available as their prerequisites are met, none of this random maybe or not (unless this is some bug), with magic research would be at a 20% bonus. and all others at a %20 negative, with none of the super rare techs available.
You could also chose no specialty, no penalty and stays the same.