After Effects has a panel problem
After Effects has a lot of plugins that can really speed up animator's workflows. When functionality is missing, plug-ins and scripts fill the gap. Unfortunately the After Effects SDK makes most helpful tools keep all of their functionality contained within a ScriptUI panel. This is fine for really big tools like Flow and Keysmith, where you want to integrate them into your workspace because you use them all of the time. However, there are a lot of "single-use" tools that only do one thing, but need a full ScriptUI panel to display a control of some sort. These can add up quickly and take up precious screen real estate for a program that really should be only a few panels.
I've attached a screenshot of how bad it can get, although I doubt anybody has actually gotten to this point. It looks like if somebody installed a million toolbars into Internet Explorer! It's got to the point that aescripts themselves have made April Fools jokes about it (Plug-n-telligence). You may think increasing the resolution can fix it, but even that doesn't fix the problem. Even a reasonable workspace can be a headache! This "ScriptUI ****" really comes down to 2 problems.
First, ScriptUI panels are allowed to be too big. A lot of scripts like to have big, cozy buttons that really don't need to be that big. Allowing us to manually set the scale of a panel could really come in handy. However, some script developers do take this into account and make buttons that can be small, like in Hylian and Mobar. The problem with these is that they need a title bar, which can often be bigger than the panel itself! Allowing us to hide a title bar for a panel or panel group would be really helpful in cutting down the size.
The other side of the problem is plugins that you don't need all the time, but are nice to have within reach, like EaseCopy, Hylian, MatchRate, Buttcapper, etc. Closing these and reopening them from a menu is inconvenient at best, especially if you have a lot of ScriptUI panels to scroll through. It's bad on Mac, but even worse on Windows where you essentially have to bang your mouse against the bottom of the list to get it to scroll. How can we solve this? It turns out we already have! In Illustrator and Photoshop, windows can be minimized to a sidebar and popout when needed. This would be helpful when, say, editing text. I don't always need font adjustment, but it'd be nice to have in an easy-access panel without having to re-enable the panel. I don't always need the Effects panel since I mainly use FX Console but a list comes in handy cometimes. Maybe we could make contextually-aware panels? Perhaps Penpal could appear when editing paths but change to a different panel when not? It'd also be nice to open panels with a keyboard shortcut and toggle them off when done. Maybe you can even allow scripts to add themselves to context menus?
I'd love to hear other's ideas on this but overall I think the ScriptUI problem needs to be addressed, especially since (small screen) laptops are becoming ever more common for animators now.

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Bruno Quintin commented
I noticed that the toolbar is actually a panel without a title bar. If I move it, the title reappears. So it should be possible to hide the title bar in the panel options, or it should be a possibility in the script itself (this would be really nice for a script like KBar). It should be possible to create custom buttons in the toolbar and also to customize the tools at the bottom of the composition viewer (like in Premiere pro). Introducing in After Effects the same system of reducing panels to icons as in Photoshop and Illustrator would be really nice!
I'd like to take this opportunity to point out two stupid things in the interface: the option of small tabs in the panel options (but who needs large tabs) and the fact that in 3D the viewers use the same buttons at the bottom, when there should be these buttons for each viewer.