I have been using selection for two years exclusively now and whilst it may have a learning curve it is worth the effort, for me at least. Many of the top players don't use/need it.
Can you indicate what screen resolution you are designing for? Because foldit doesn't use a GPU it runs well without a dedicated graphics card, but on a 1024x768 resolution, which is a Windows default res, the on screen clutter is overwhelming. http://fold.it/portal/files/chatimg/irc_179219_1379119423.png Note that this is my current set up because it gives me access to better compute, but nearly all of the items below are a also a problem on a very high resolution. I tried fade gui but it was way too busy and distracting and hid the things I need to see, like script output and behaviour box.
Cartoon thin or cartoon thick? I prefer thin, so I can see round helixes, the selection lights up in blue thick, both obscuring the colour clues provided by the aa colours and creating a disjoint in size when you are trying to line things up with non-selected pieces. Recipes, apart from Pletsch's My GUI script, select all so you get a cartoon thick in blue again robbing you of valuable information. Not sure if there is a way to stop scripts doing this. Does anyone use cartoon thick?
The throbbing box top left uses a lot of real estate - essential to check that it hasn't frozen but could be much smaller, maybe a bar style?
Moving horizontal buttons, this effect is very annoying to me,especially when using bands in combination with scripts, disable bands button moves about. Addition of idealise and move select (grr) push the buttons so far across the screen that I have to open notifications window to access the chat open/close triangles. Also I have hit rebuild instead of idealise a couple of times :) tiredness, a factor of playing late trying to set up for a long script.
Vertical pop up menu - appears to be appealing to a childlike audience which is inappropriate for an 'advanced' interface. Also view and undo buttons are cunningly buried under the enormous Script running box, which can't be moved. View and undo need to be accessible.
View menu is huge, can it perhaps be setup so that there is a separation beteen items which you never change once set up, and things you need to get to all the time. So that you can expand it to access those items on the rare times you need to use them?
The distribution of tools across the main menu and undo menu appears to have grown a bit like topsy, so often you need to have both open and look at a postage stamp size protein.
Many of the tools could be set up in the same way as the original interface using the side attached triangle open method. As long as they are grouped so they are accessible when running scripts. Behaviour I have open alll the time for example but don't like having to move it out of the way.
An advanced GUI can have a learning curve, and not be entirely 'idiot proof' imo, crashing or making an error because you do something silly is not a bug in the software as such.
You can do stupid things in most software, for example Word, spreadsheets, graphics and CAD.
I would prefer the scientists to have the best tool they can get and try to use some of the tricky bits myself, rather than reduce the tool functionality to the lowest common denominator user. Not sure if they use the scoreboards or chat options though :)