gmailmacosmail.app
This isn't a new problem with OS X Mail, it persists into Mountain Lion.
The badges are quite obnoxious; I can go into that [Gmail] folder and right-click and Mark As Read. But they start piling up right away again.
Is there a way to never have a badge beside any non-Inbox folder, or have a way for Mail to automatically clean up?
Go To Mail -> Preferences -> Junk
When junk mail arrives, say: Perform Custom actions
Click on the Advanced button at the bottom, which just turned up to be active.
Then say "Mark as read" in one of your actions:
Before you completely ditch GMail and go just with your iCloud account, you'll need to ask yourself this question:
Will you only access your mail solely from Apple devices?
I for one created an iCloud e-mail account on my Mac just to be disappointed that I couldn't configure my Android phone to access it. Probably Apple is not using standard IMAP for its iCloud e-mail service.
That said, you could upgrade your GMail account to a premium account to get better quality of service (and perhaps not having them selling off your e-mails).
Best Answer
Create a filter in Gmail (web settings) to automatically mark all spam emails as read.