High wimpy is annoying as hell for transmuters. Neurological disruption is a big lag spell without dealing much damage. If you keep fleeing at 50% hp, they're using a lot of time and mana if they keep trying to hit you with neuro. Still, if you are low int/dex and lower level than them, you're generally going to struggle because it's just a bad matchup.
A few ways to deal with them-- first and foremost, always dispel them if you can. Once they lose their malleability/quickening they will run or die. Even better if you can drop their fly/control and trip or bash em along with their own failed neuro lag. Disarm or otherwise weaponbreak can also do wonders but again you've likely got to drop their spidergrip. Also, they're probably geared heavily for hp and relying largely on giant strength to keep their strength up. Stacking some maledicts can drop their weapons pretty quick. Eagle staff is very heavy and does not take much to drop. Time it right after their neuro fails; if they've spammed a neuro or two and suddenly lose their key spells and get lagged out of rythym the fragile races go down mighty fast.
Next, do not underestimate the amount of spells/mana a muter is trying to balance at any moment. Neurological disruptions take a lot of mana and if they haven't timed everything perfectly (especially pre-hero ranks) they will be juggling many spells with very limited mana and trying to strike you in a perfect window of time, which means various spells can fall mid-fight and you can occasionally catch them on that with a bit of luck.
As for protections, they have to pop out of duo to use preps so depending on their willingness to sacrifice that element of surprise they may or may not be fully prepped. If you keep checking "who" you'll have a sense of this. Making them think they have the element of surprise can work to your advantage, as can quickly checking the adjacent areas when they pop out to prep.
For the high int/dex muters , they are typically going to be using malleability, metabolic quickening, and adrenal burst. They lose movement extremely fast if fighting more enemies (including mobs). Have a pet, set up an ambush. Against a bunch of zombies they may only have a few rounds before they pass out from exhaustion.
The toughest transmuters are always thinking in terms of a sequence. Neuro, slow, neuro, soften, mental jolt, neuro, neuro, disrupt f, disrupt o. If they hit those first few spells (before the neuros start) just run. If they miss one or two be ready with a strategy.
Also, keep them glowing and/or bleeding. If you can get lucky and knock them out of duo with fog or whatever, they'll be lagged and if they've slowed themselves or let any spells down and you catch them like this you can quickly smoke them. Transmuters hate losing their exit strategy they get so used to-- keep them glowing and cursed.