Yea the spiders can sometimes get confusing. A lot of money to spend to hope they actually make webs. I think a lot of masterwork is getting rid of the frequently used linear tier system of better vs worse. In vanilla once you had steel you would completely ignore anything lesser. In masterwork there are alternatives just as good or slightly better/worse than steel in some aspects, but then a much better weapon or armor in another aspect. Adds a lot of variety.
It's a little trickier with the animals. The manual dedicates some time to each of the unique dwarven pets, they are worth taking along for fast meat production, booze from milk, shearble fur and metal grade scales, extra furiousity in battle, etc. The rest are very much for flavor and mysterious challenge. There's so many animals I don't think you'll ever really find a table that you can pause and look up that "random animal type here" beat drake in 1v1 fight 62% of the time. As Meph suggested before with the new armor types and metal he tried to balance everything with their name. A legendary blood sword of armok will beat out a rusty iron sword any day.
For creatures I'd also suggest looking at their body size, if that is still visible. Maybe take note of how fast they move across the map and if they are known for some horrible poison. All in all I think it's the variaty that makes the game replayable. I think most of us came here because we were sick of the same old routine, waiting for the only enemy the goblins to show up, get iron, get steel, get candy, avoid tantrums and done. Now when I play I hardly see the same creature twice and never know what my dwarves are in for.
Is there a certain reason you're worried about this micromanagement? Are you trying to focus on high value foods from meat or something along those lines? I'm pretty sure the manual covered ones are the only really special ones to worry about unless you start playing one of the other included races.