For maximum server compatibility, we need to switch from using /wp-json.php, as some server setups cannot handle this correctly.
One of my nginx setups parses /wp-json.php/posts and tries to load wp-json.php directly without falling back to index.php afterwards. This could be an error on my end, but I'd bet it's fairly common.
The original point of this was to ensure that the API endpoint was always at the same place, even once merged (and assuming that wp-json.php gets dropped into the WP root directory). However, with support for RSD (#40), this isn't an issue. I'd rather we change it now in that case.
I think /wp-json/ should be a fairly non-conflicting endpoint (with /wp-api/ to be used eventually per #34).
Somewhat related to this, I'd strongly recommend placing a version number after the endpoint, like /wp-api/v1/ so future breaking changes can be implemented while maintaining backwards compatibility with earlier versions.