Like Tony, I'm not experiencing any significant issues with ISOs not resuming regular playback.
I tried your scenario (play ISO, exit, play MKV, exit, resume ISO) and it worked fine. I'm also streaming from a network share, not playing locally.
I then tried to open another ISO that I half watched last week and (to my surprise) it offered to resume and then resumed playing in the correct place.
My tests are resuming from within the movie, not the menus. I'm not pausing or stopping the movie first; I'm simply hitting the Back button during playback to exit.
You can make an ISO fail resume (actually, it'll auto-exit playback mode) by first taking the playing movie back to menu, then exiting, playing another file and going back to the ISO to attempt a resume. It correctly resumes back to the menu but fails to resume play, instead exiting the ISO. This is duplicable; happens every time.
So there are some issues with ISO resume in more convoluted circumstances but, for regular resume of playback, ISO are working fine for me.