The fix for the intellisense issue will be in VS 2005 SP1.
In the meantime there are two workarounds that you can use to fix it immediately:
1) Keep the .master file open within the Visual Studio IDE when working on the .aspx content page. It turns out the intellisense engine only runs into issues if the .master file is closed. As long as it is open within the same IDE, it resolves the assemblies just fine and will give you full intellisense
2) Go into your web.config file and change the tag-prefix naming for the ASP.NET AJAX controls to something other than . For example, instead of:
<controls>
<add tagPrefix="asp" namespace="Microsoft.Web.UI" assembly="Microsoft.Web.Extensions" />
<add tagPrefix="asp" namespace="Microsoft.Web.UI.Controls" assembly="Microsoft.Web.Extensions" />
</controls>
change them to something like this:
<controls>
<add tagPrefix="ajax" namespace="Microsoft.Web.UI" assembly="Microsoft.Web.Extensions" />
<add tagPrefix="ajax" namespace="Microsoft.Web.UI.Controls" assembly="Microsoft.Web.Extensions" />
</controls>
You'd then want to update your tag prefixes in your .aspx page to use this new tag prefix.
Either of these approaches will solve the problem and deliver full intellisense. The issue should then be resolved completely with VS 2005 SP1.