@westfw Good question.
I have made as much of this plugin (all the arduino stuff) a separate api and have ensured that all the Arduino/Project settings are not tied to any Visual Studio settings. So actually it could work with any IDE in the future.
Although Atmel Studio lacks a lot of the nice features of normal Visual Studio systems it isn't that far away in terms of what it might do for us. Much of the user interface provided by the plugin would probably work "as is" with Atmel Studio it might only be the areas that modify VS CPP properties (to detect Arduino sources and set board properties) that would need to change. This is an easy change because VS 2008 and VS 2010 use different CPP systems so the code is already conditional in this area. However with the proper support from Atmel we could really tap this stuff into their IDE and integrate it fully.
The problem is that Atmel are not a proactive company and their developer support is poor. I only have a few questions for them and have approached them a number of times. Each time I have been promised that developer support is planned for some future time. Not very helpful! I am sure I could work it out by myself but time is the limiting factor.
If anyone would like to help with the understanding of the Atmel side of things I would be more than happy to give it a go sooner rather than later.
So far, this project has cost a lot of time and money which makes it difficult to justify the addtional time for Atmel studio right now. For obvious reasons there is no support for this project from Arduino or Microsoft 
This is why the new Arduino debugger tool is not going to be free (but is free and in beta at the moment). I hope the revenue from the debugger funds the time and provides the motivation to make this plugin work with Atmel Studio.