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[NEANDERTHAL]

Director of Research would be a noble position which would mandate the research of certain topics, as elected by the scholars/appointed by the crown/player.
Rather than an unfulfilling and gamey "tech tree", or research that consists entirely of historical or otherwise non-interactive work (astronomy, levers, etc.), scholars could also compile scientific data on things like the specific weights, volumes, and abilities of forgotten beasts, experiments, undead, wildlife, and the appearance and behavior of living figures i.e. vampires and warmongers, based off of the accounts of citizens, soldiers, liasons, and dedicated research missions. This data would be directly availible to the player by examining books like "On [Hist fig/FB]" and "Fauna and Haunted Weather of [biome]". In general, scholars could retrieve legends info that is more relevant to the fort than odd historical events.
Maps could also be created, again using legends data.
Caravans could value books based off of their content (guides to territories they're interested in, research on animals/people that align w their spheres, etc.)
Manuals could be written (by guilds?) describing certain processes and added to workshops to improve learning rates. Certain jobs (gem-cutting, strand extraction, elven growing magic, animal training, etc) might be prohibitively difficult/expensive to learn without a manual and/or instructor, inciting a need to send dwarves away to college/host a college of your own.
Imagine getting lucky with a voted director who likes the forgotten beast sphere so you can be prepared, or having to magma a director whose only interest is the local herbs.
Caravans would value books based on their content relative to their civs knowledge corpus and spheres. Elves would love a scroll on the climate of a prospective territory but reject a manual on growing methods, etc.
The crown could give grants/pay premiums/threaten the fort to keep certain knowledge inside the civ like FB info, etc. (or perhaps keep secret the appearance of an ancient vampire who disappeared shortly before the king's succession?)
Research could play a role in the outcomes of hist gen battles. Art/poetry could shift the values of a whole civ.
Demonology/Angelology would be an interesting field.

[betaking]

Ideas for innovation would work if there was any sense of "strategy" or "borders" beyond mere settlements.

That said with regards to "innovation" I think having some kind of prescientific method-based approach, something that is capable of giving "negative reactions" as well as "positive reactions" might be good, there needs to be some kind of object for "philosophy" or "rules" or whatever.

Example: a "Pythagoras"; you get a^2+b^2=c^2 for calculating the hypotenuse or whatever, but he also hates beans, so like you lose the ability to grow beans until/unless another philosopher comes along to challenge it. Other times you get things like "Realizes the world is round" but "convinced that dolphins are in fact fish and animals spawn out of thin air" or whatever.

[Azerty]

Ideas for innovation would work if there was any sense of "strategy" or "borders" beyond mere settlements.

That said with regards to "innovation" I think having some kind of prescientific method-based approach, something that is capable of giving "negative reactions" as well as "positive reactions" might be good, there needs to be some kind of object for "philosophy" or "rules" or whatever.

Example: a "Pythagoras"; you get a^2+b^2=c^2 for calculating the hypotenuse or whatever, but he also hates beans, so like you lose the ability to grow beans until/unless another philosopher comes along to challenge it. Other times you get things like "Realizes the world is round" but "convinced that dolphins are in fact fish and animals spawn out of thin air" or whatever.

The main fields of philosophical doctrines might be ethics (i.e. ethics, goals, facets and cultural values), metaphysics (i.e. positions on the nature of the world such as life, mind and things) and epistemology (i.e. how to get knowledge: revelation, experimentations, reasoning?).

[NEANDERTHAL]

The issue is that having scholars study philosophy/mathematics/unimplemented mechanics all day, like they do now, or ancient/irrelevant history, misses out on the potential of a natural/scientific/political research mechanic. Imagine being able to read an encyclopaedia of all the clowns and their stats (weight, abilities, description, etc.) compiled from survivors accounts of goblin leaders before you breach the circus, or sending your children off to college in the mountainhome to return literate master miners who can write manuals.
side note: literacy should be a skill dwarves have to learn in fort mode, from a literate instructor/college.
also: research directors should not be able to ban beans. they are research directors, not mayors etc.

[Maximum Spin]

side note: literacy should be a skill dwarves have to learn in fort mode, from a literate instructor/college.

This is silly. Research has pretty clearly shown that random medieval peasants were usually literate in the vernacular; we have personal documents written by such individuals.

[Azerty]

The issue is that having scholars study philosophy/mathematics/unimplemented mechanics all day, like they do now, or ancient/irrelevant history, misses out on the potential of a natural/scientific/political research mechanic. Imagine being able to read an encyclopaedia of all the clowns and their stats (weight, abilities, description, etc.) compiled from survivors accounts of goblin leaders before you breach the circus, or sending your children off to college in the mountainhome to return literate master miners who can write manuals.
side note: literacy should be a skill dwarves have to learn in fort mode, from a literate instructor/college.
also: research directors should not be able to ban beans. they are research directors, not mayors etc.

I agree, there needs more scholars doing studies on things such as dissecting creatures, studying stones and describing plants.

But technologies need to be related to the various topics.