Logic's big problem for me is that it betrays its MIDI-only origins so blatantly.
The Environment, for example. Great for hard-core MIDI (linking things together, arpeggiators, all that nonsense); unnecessary bloat for audio. What audio routing options are possible in Logic that are not possible in the simpler, environment-less Pro Tools? Why is it ever useful for me to have two copies of the same audio track in the environment?
Audio editing, as well. Despite the clunky fudge known as the "Marquis Tool", Logic still treats Audio regions like MIDI regions, that must be chopped before they can be moved.
Apple are famous for "sweating the details" - all the tiny little things that make your workflow faster and more enjoyable. They NEED to do this in Logic, like Digi have with Pro Tools. To provide one simple example: after all these years, I still can't fathom where the screen will be focused when I zoom in (using keyboard shortcuts). Pro Tools zooms in on the place you have selected, or the last place you were editing - it always just seems to zoom in where you were looking. And don't get me started on what happens when you zoom out.
Another example: I want to import stuff from another session. In Pro Tools I just go to "import session data" and it is beautifully easy. In Logic it is a nightmare. Even the simple act of pasting regions into the session is a faff. And as for, say, trying to import all the drum settings across a dozen tracks...
One last example: the difference between Logic and PT when I click in the scroll-bar to jump a page to the right. PT jumps a bit less than a page, so I can still see where I was; Logic jumps the entire page, losing context, and I always find myself manually scolling back a little. Thank goodness I bought a mighty mouse.
I love Logic, and I use it every day. But I still curse it every day. It needs a real re-write. I'm happy to relearn some things if they actually Apple-ify it.