At the time I struggled to find an official release from Microsoft commenting on this change – it seemed like a breaking change that caused issues in a number of deployments so I was surprised this wasn’t sign posted more explicitly (maybe I missed something in the release notes :|).
In any case it appears this may now be changing – at least in respect to load order. In the release notes of Rollup 15 under ‘Issues that are resolved in Update Rollup 15 for Microsoft Dynamics CRM 2011’ there is this little nugget:
Loading order of web resource script files is not respected after Update Rollup 12.
It’s difficult to tell exactly what this means and what change will occur, however it definitely suggests that the load order will now be respected (even if they do load asynchronously), which seems like a good thing.