Personally I like instrument tracks. They're not perfect and have their downsides - but nothing that can't be solved by temporarily splitting them, doing what you need to do and joining them again. One example is flipping the stereo interleave button, which for some bizarre reason the Bakers decided to leave off instrument tracks. There are some other documented oddities, like unexpected behavior when cloning an instrument track for instance.
But aside from this, I like the tidiness and convenience of them. They take one lane in your arrangement as opposed to two for an audio/MIDI pair. This makes a huge difference for me in terms of organization. You can have so many more tracks of your arrangement visible at any one time and everything is much tidier.
I'm not sure exactly what isn't accessible on instrument tracks, but most of what you need is contained in the Audio/MIDI tabs of the inspector. For everything else, like I said, it's no bother to just split the track temporarily and access what you need.