the advantage is much easier maintenance. the disadvantage could be that you can't see the whole configuration in ~/.wine/config file anymore - some settings could be overwritten by optional file in ~/.wine/app-config.
well, what I don't like too much is the time at process startup to look up for the correct file (if it exists). Especially if people start writing app specific files like rabbits. Couldn't we put a speed up in the file look up ? Something easy like naming the config file after the first letter of the application... (I know it'll break *foo.exe, but it shouldn't be too much of an issue). Future work may also include version information if available (think of winword.exe for example ; all of those are rather different apps)
regarding configuration, another point which really bugs me is also the content of the registry. I fear this is going to cause us lots of trouble in the future... and may be we'll need application specific keys in the registry...
A+