There is quite a bit on the web the last few days about Apple Mail's support (or lack thereof) for Gmail. Joe Kissell has been at the front of this over at TidBITS. In my mind Apple Mail and Gmail have never been like chocolate and peanut butter together. They are, in reality, much more like oil and vineger. Apple Mail has matured and developed into a pretty terrific IMAP email client. The rules engine is unmatched and features like VIP and Smart Mailboxes have become essential to me.
The problem is that Gmail is not an IMAP service. Neither is it POP. Gmail is something entirely … well … Google. While in the past people have been able to get Gmail working in Apple Mail it always involved copious amounts of scotch tape and chewing gum. Apple has never had any interest in building in support for things like Gmail labels and inbox filtering to Apple Mail. Why would they?
If you use Gmail, you should be using all of its features. Google has done some really useful things in their email sandbox over the years. You will never be able to use those features in Apple Mail. So my advice is to get over it and move on. Use the browser for your Gmail accounts or something like MailPlane, designed around Gmail.