My issues with the store apps are that most of them act like "apps" and not like "programs/applications". For example, they close on their own with no warning. I tried to use the store version of the Pandora app, but it would be closed when I left it paused for too long. Same with Facebook's Messenger. I don't want that. I want to be able to control when I open and close a program.
That doesn't happen to me with the messenger app...
My biggest issue is the amount of unofficial apps that look official. It's a trust issue. If I go to the website I at least know that I'm getting legit software.