While I don't have so few mailboxes, my "system" would be easy to use to alleviate the problems he is describing.
Basically, I have decided what kind of messages that are of interest to me. I get about fifty to a hundred mail messages each day of varying importance. So basically, out of all these messages, the important ones are:
So, with this in mind, I've created a smart mailbox that I call "Current". This is my home in Mail. I've set mails unread count dock badge to show unread mails in this mailbox and this always shows me a snapshot of everything that is important to me.
The most important part is that I can still continue to use filters to automatically funnel mails to special mailboxes, which is important to me. I have a number of rules set up that saves mails in special mail boxes - such as mail from specific people or groups in my address book, but also mail that are related to order confirmations and such.
So I can't count on the inbox alone. But this smart folder has really done wonders for me. At any given time, I have top 50 mails in it, and that's when most are unread. When I read a mail that I want to keep in this mailbox for further processing later, I flag it.
Obviously, this rule could easily be altered to incorporate mails from a "Flagged" mailbox where mail on the iPhone have been moved. I mark mail on the iPhone unread that need further processing back on the desktop, but that's me.