Hey,
we looked into simplifying the GUI before (and came up with the presets system that let's people tune the configuration via a slider).
Unfortunately the plugins need to be setup individually on top of that.
Everything in PCSX2 design is built on the idea that having the option to change things is always better than forcing one default on the user.
As such there's now a staggering amount of options available and some in the dev team agree that it's "too much".
Modernizing the gui would be a great opportunity to fix things but there's one big problem with that:
GUI work is boring and hard and unpopular.
It's therefore pretty unlikely that you'll see a new GUI from us but, as PCSX2 is FOSS, anyone that wants to tackle it can do so and we'll gladly help the process
Simply improving the current GUI is also an option and many of the things suggested here can be done. It wouldn't even be hard to implement
since there are improvement attempts already in the code. (GSdx tooltips for example)