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The frameworks that AFT uses are open source if anyone wanted to make a better one :P

You've given my life purpose. By that I mean, AFT is the worst application I've used in my life, ever. It is that (un)reliable. And I need yet another side project.

Although not an ideal solution, I just use Airdroid when on OSX.

http://airdroid.com/

for my S3, I use an app on my (rooted) phone called EasyUMS to enable Mass Storage mode.

The other option is to try and find a better app that supports MTP.