The main problem with their mocap is the walking animations. They look a thousand times better in the latest footage but still off for some reason.

I think they're getting better. This game does look noticeably more fluid to me so far.

I noticed the male motion capture actors for female characters in MKDA. It's especially noticeable with Sonya (which is odd given the number of female Tae Kwon Do experts) and Li Mei; Nitara's body masks it pretty well.

I think one of the problems was probably the diversity of styles they used. I'm not exactly sure who did their motion captures, but I'm assuming it was more than one person and that they looked for people who could pull off the different styles.

Now that they're not doing the styles anymore, maybe the pool of available female motion capture artists will be wider.

The reason for that is the motion capture actors they were using were guys who already worked for Midway like Carlos Pesina, so they didn't have to hire anyone extra. Games are expensive and Midway was never financially very well-off, obviously given they went fuckin' bankrupt, so money saving tactics? Kinda important. Also note that in most of the games, the voice actors are, again, pretty much the developers themselves.

That said, for MK vs DCU they did hire actual actors of the appropriate gender to do the voice acting and the mo-cap for the story mode cutscenes (in fact, Raiden's VA is somewhat famous for all the anime he's done, and Shang Tsung's was Ando from the TV show Heroes), so who knows. They may be employing actual outside assistance, including females, for the moves too in this generation.