I find SEO, even just META tags with key words, to be a little difficult when using ASP.NET with masterpages. Am I missing something?
I wouldn't worry too much about meta tags. They're nice to have for completeness but their effect on rankings has diminished. (Sorry, it doesn't really answer your .NET question!)
Is your problem that you are trying to change the meta-tags for each page. You can reference the master page from the child page, so just drop a literal control on the master page in between the meta tags and update that.