You can bypass MTP with ADB. A dirty method, sure, but it's worth the ~ 10 minutes to set up because it'll work with just about any future Android device as long as the development options are available. And then it's just as simple as:
1. Connect the device
2. Open the Terminal/ADB
3. If you want to install an app:
Code:
adb install draginyoursaidapptothewindow.apk
And then press ENTER.
If you want to push some files/folders.
Code:
adb push lalala.pdf /sdcard/
And then press ENTER.
If you want to pull something out, like all your photos:
Code:
adb pull /sdcard/Pictures/
And then press ENTER.
I don't do the whole plug in your device, mount the USB drive, dig through the folder/open the app thing. It takes too long.