How about just a flat bonus to the specified resarch type, then?  Like Plus 8 or something...  Just something to make the world a little more interesting.

I'd like the idea of themed lost libraries, but instead of a research bonus to specific branches, I'd like to see them give you a unique technology of the said branch.  i.e. warfare gives you access to some kind of unique weapon tech or something.  You could protect them with powerful guardians to keep them from being game-breaking in the early game.  I think it could be fun and add some flair to the questing and lore of the game.

Here here, good concept.

You could even make them progressive by tying the benefits to tech levels.

Low-level utilization (available to undeveloped players) - grants bonus to spell/magic research, maybe even a low-level unique spell unavailable in spellbooks.

Moderate-level utilization (available to moderately developed players)- grants increased bonuses, etc.

High-level utilization (available to advanced players)- grants increased bonuses, perhaps some unique high-level spell or unit (like a Mana Golem or some such)

If you wanted to restructure the game more deeply you could even have the sites hold parts of the Spell of Making or the Master Forge (these would of course be available only at the highest levels of development).

This would keep them relevant throughout the game as locations to be held by those who have them, and as sites of interest for those who dont.

I'm all for increased variety just for varieties sake.  I'm also interested in things which offer more choices of opportunity.

I'd enjoy seeing Martial Art Academies, Farming COOPs, X Mage Collectives, Stewardships of Knowledge, etc etc.  ..Various resources which represent specialised NPC communities which the player can align with by incorporating them within a cities border.  These resources aiding research into specific tech trees, and perhaps for particular techs.  I've pen and papered some thoughts for future modding once the game gets more stabilized.