Reddit reviews Feast of Souls (Magister Trilogy, Book 1)

I would suggest C. S. Friedman. She has a lot of the flawed character thing going on in many of her books. She does a bit more sci-fi than fantasy, but honestly either way she's great.

This Alien Shore is good, and a stand-alone:
http://www.amazon.com/This-Alien-Shore-C-S-Friedman/dp/0886777992/ref=la_B000AQ1TUO_1_9?s=books&ie=UTF8&qid=1410005630&sr=1-9

Feast of Souls is the start of a good trilogy:
http://www.amazon.com/Feast-Souls-Magister-Trilogy-Book/dp/0756404630/ref=la_B000AQ1TUO_1_5?s=books&ie=UTF8&qid=1410005630&sr=1-5

And Black Sun Rising is also the start of a good trilogy:
http://www.amazon.com/Black-Rising-Coldfire-Trilogy-Book/dp/0886775272/ref=la_B000AQ1TUO_1_1?s=books&ie=UTF8&qid=1410005630&sr=1-1

The Tamir Triad by Lynn Flewelling. Protagonist female but magically disguised as a male at birth and believes herself to be male throughout a portion of the trilogy, so that may disqualify it for you. I really enjoyed it though, and there's definitely some fun upsetting of gender tropes going on. Despite the premise and the existence of Wizards, most of the central plot is relatively low-fantasy, and there's nary an elf nor dwarf to be seen.

Also, The Magister Trilogy The trilogy primarily follows the adventures of 3 women, one of whom descends from a mythical caste of warriors and becomes a warrior in her own right later in the series. A higher-magic world than Tamir, but the narrative is darker than your average high fantasy, and there are complex female heroes and villains in spades.