I don't think all my raw fixes apply now that animals have changed in the new version, but historically I always:
remove all exotic tags from every animal in the game
remove all grazer tags (i used to just reduce the amount of grazing on animals that need a lot of space, but nowadays I take them out altogether. Just too annoying)
add trainable to a variety of my favorite animals and all megabeasts (elephants, unicorns, cave crocodiles, eagles, etc, then also hydras, colossi, etc)
remove all vermin_hateable, vermin_eater, vermin_rotter, and penetratepower tags (wretched vermin!)
remove the cat tag that lets them pick their owners (I MAKE THE DECISIONS AROUND HERE, FELINES)
render all plants inedible to vermin (wretched vermin.), and make rock nuts inedible (quarry bushes are too valuable and I don't want my dwarves eating all the seeds)
make all six of the dwarven plants growable in any season
boost herbalism cluster sizes for several of the best wild plants
mod out the [good] tag from sun berries mainly because they're so valuable and I like to have a chance of finding them wherever I go
mod in liaisons for elves and humans (being able to make agreements with them is really awesome - esp being able to request rare animals from elves, eagles and unicorns for example - and I would never get those liaisons unless I modded them in myself)
remove all demand_max and mandate_max tags from nobles (dear nobles, you are the enemy of my civilization and i will use any tools available to render you powerless)
remove treecap diplomacy (I MAKE THE DECISIONS AROUND HERE, ELVES)
remove skill and attribute rust (too annoying to get around with some skills, like medical skills)
remove several examples of trapavoid, canopendoors and buildingdestroyer on hostile creatures (I avoid taking it off of the really powerful creatures, but small timers do not deserve this power if you ask me)
speed up childbirth for some megabeasts (dragons, hydras)
remove all aquifer tags (waaaay too annoying for me. I always embark on a river so water is not an issue)
add a workshop that trains several skills for free, and add all its required reactions to entity files (this is cheating imo, so I try to use it very sparingly, but some skills like siege engineering and medicals are just too difficult to train by "fairer" means. I also use this to improve the skills of freshly arrived migrants, to make them useful to me without having to waste raw materials on them)
Also, as I go, I write down every change I make to a tracker file so I know what raw edits I made for future versions. Some day I'll script this stuff out instead of making all the changes manually, but in any case I want to know what edits I made from the original raws so I write them all down
Make scales and chitin tannable to leather and tanned chitin
Make several different versions of leather, bone, and other structural materials, and assign them such that larger creatures have stronger materials (so dragon hide is much tougher than cat leather)
Apply some experimental reactions that make large creatures give more than 1 unit of leather
...
Make giant animals and animal people much, much rarer
Remove sponges (and giant sponges and sponge men) from the game completely
^ I definitely need to try some of these