I have used .Mac, MobileMe, and now iCloud email, and utilize the Apple Mail app for pretty much all of my emailing needs. It has some limitations, but just like Notes, Pages, Numbers, etc; I really prefer to keep everything native if possible.
Right now, I have about 20 filters in Apple Mail, which seems to be performing better in regards to spam/bulk mail overall; I usually receive about 10 junk mails per day, but I also have a junk@icloud email address that I use only for newsletters, signups, etc and reserve my primary Apple ID email for family, friends, and other trusted sources. This has cutdown on my spam mail over the years.