I love it mainly because I can keep multiple explorer locations open for different projects I'm working on, without actually having to sift through tons of different open windows. I've also gone through the settings and found several little things that help, like being able to instantly clone a tab by using a custom click on it. I also love that it will open the last set of windows I closed when I start it. I can see how you wouldn't want to use it if it was just keeping drives open, but I use it so much I start to feel really unproductive when I'm working on other computers without it
And I agree that it is very stable. I don't think I've ever had a single problem with it.
I think your issue with the folders going inside sub-folders is a problem the author is aware of and planning to fix. Then again, there hasn't been an update to it since like August of last year, so who knows when that'll be...
7-zip also has a fairly nice "file manager" interface built in. I certainly wouldn't recommend it as replacement, but I've found it to be useful before, mainly for easily navigating through compressed files and folders alike, without having to pause to extract every compressed file you want to look into. probably not what you're looking for, but worth mentioning.