I will like to thank Chris Doty for creating the WSPDeploy project. The new tool is basically a console app. that can deploy SharePoint solutions. The good thing about it is that WSPDeploy uses a library and therefore makes it easy to create a winform app. on top of it.
The 0.9.7.0912 release
This release has primarily been about the auto detection of Security Attributes and is now supported to some degree. But there are still a lot of issues to be solved. Like it can only detect the first Attribute and use this, all other attributes of the same type gets discarded. Therefore if you are not sure of what you are doing with the Security Attributes, use the Global Assembly Cache instead.
Get the latest release here: http://www.codeplex.com/wspbuilder .