PBA:
I actually think low self esteem is a lot worse than an individual bad middah because if a person suffers from low self esteem or rather very low (because we all suffer from low self esteem to some degree except maybe a few Gedolim here and there) it takes over the persons personality and effects all their thoughts, feelings and decisions and middos. Having low self esteem and acting a certain way because of it does not negate the notion that the person has bad middos. Self esteem issues does not give anyone a right to have temper tantrums and treat others like trash. Its not an excuse to do what you want.
However self esteem can be built up by working on ones middos. The process of working on middos and building ones self control leads one to have a greater sense of self respect and self esteem is the result of having a healthy dose of self respect.
Another point about Middos. We are all born with good middos and bad middos. It is our job in life to use our good middos to build up our bad ones and perfect the bad ones through that process. So no there’s no such thing as a person who doesn’t have bad middos. Just some have worse middos than others, and some middos are just very glaring and in your face like arrogance or anger…and some people hide their flaws well but those close to them are well aware of them.