I see your point on the process of translation. I certainly don't mind if developers choose to use App_LocalResources for modules that they develop/contribute going forward. When I converted the project to the 2.0 .NET localization, it was a huge job doing copy paste from the old .config files into the new .resx files. I did this for the 6 or 7 languages and it took 3-4 hours for each one. It would have been an even bigger job if I tried to split it out into separate files at the time.
I think the naming convention helps for those that want to only translate a few modules but I realise I wasn't entirely consistent in the naming and some things were re-used accross pages/user controls in the past. I do want to encourage complete translations as much as possible.

The other option going forward is still to use App_GloableResources but for new features create a new FeatureNameResource.resx file in App_GlobalResources
This would keep at least all the resources for a feature in one file.