User interface paradigms that need changing?
Clicking things on touch interfaces
It's incredibly difficult to click on things on a touch interface, because you don't know when you have pressed the screen hard enough. And if you add an animation to the button you are clicking, you most likely wont see it, because your finger is in the way. Adding other reactions, like vibrating the phone or painting waves on the screen might work, but there is usually a delay which is too large, much larger than the tactile sense of a button being pressed. So until they invent a screen with buttons that can be pressed, all touch devices should move towards dragging user interfaces (DUIs) instead.
Counter intuitively it is easier to press an object on the screen, drag it, and then release it than it is to just press and release it. It's probably because you can see the object moving when you start dragging, and you can adjust the pressure while dragging it. Dragging also has a lot more options, because you now have a direction, not just a point that you clicked. You can do different things if the user drags the object in different directions. Speed might also be used, as well as the point where the user releases the object. The release point is the real strength of DUIs, because it is very easy to release something, even with pixel precession.
Some designs have started to use DUIs, like (here we go) the iPhone, palm pre and android phones. But only part of their design is DUI, the rest is clicking. One area they all have in common is the keyboard. Instead of clicking on a key the user presses any key, then drags their finger towards the key they really wanted to click. Unlocking these phones also uses dragging.
Other easily implemented DUI features would be things like mouse gestures, where dragging in different directions, or drawing different shapes does different things. There are also alternate keyboards being researched which puts a bigger emphasis on dragging. All buttons can be changed into switches, so have to drag them down a bit to click them. With a well designed graphics, this should be intuitive to the user as well.
You mentioned popup modal dialogs , and I'd argue that non-modal ones are just as bad. Any dialog box remove focus from the program, they could end up behind the program and make it hard to find it, they might not even appear on the same virtual screen.
I'd like to see an end to all dialog boxes. If you need to stop someone from using the UI because of some non-normal circumstance, then remove the relevant parts of the UI from the window, and replace it with what the dialog would contain. Bring back the UI once the problem has been handled.
The Apple Human Interface Guidelines are a good read on this topic. They discuss this from a very broad point of view and the guidelines apply to any platform, not only Mac.