jonradio

First place I would look is in wp-config.php for define ('WPLANG', '');

Although Site Language has been moved to an Admin Panel (General Settings), you may still find remnants of older versions of WordPress that had WPLANG set for one reason or another.

I agree that it is a personal choice. The informed choice is really between Simplicity and Confusion. There are Reliability issues with both approaches:

1. In a Root Install, the Clutter of WordPress files and non-WordPress files that you need in the Domain Root makes it more likely that a necessary file will be accidentally deleted when cleaning up “unnecessary” files;
2. In a Subdirectory Install, WordPress Address and Site Address no longer match in the General Settings of WordPress. This can be Confusing and some Plugins will fail in subtle ways when these two addresses do not match.