Anyway, templates like in phpGroupWare would be the best way to provide easy customization, but the current design is not suitable for that. We should choose between some customization with some cfg variables and a better design allowing themes.
For 2.3.0 and not before IMO.
Actually, It's such a big work that it should come in 3.0 and not before :)
I think quite everything has to be changed. It's like restarting from scratch. PhpGroupWare people have really spend a lot of time on their kernel desing to acheive such modularity capabilities. PhpMyAdmin was definitely never designed for that. Tobias had not that time to spend on it.