MacBook Pro takes too long to boot

I have a late-2013, 15" MacBook Pro with retina display.
It takes a half hour or more to boot if I reboot it after using it for any appreciable amount of time. Sometimes I can get it to boot faster if I boot it in safe mode, or if I interrupt it by powering off a few minutes into the boot process and then restarting it.
The computer hangs on the white screen with the Apple logo showing and the spinner spinning.
If I reboot it immediately after it finally boots up, it boots normally.
I've tried everything I can think of to diagnose and fix this problem. I uninstalled every bit of software I'm not using. I removed unneeded printers and other devices. I removed all my Login items except for DropBox and iTunes Helper.
I have no startup items (both /LibraryStartupItems and /System/Library/StartupItems are empty, and ~/Library/StartupItems does not exist).
Before I got the MacBook Pro I had a 2011 MacBook Air. I used the Time Machine backup from the Air to initialize the Pro. I never had any such problem with the Air. I also have a 2013 iMac, which has most of the same software installed on it as my MacBook Pro; the iMac exhibits no issues with booting or any other problems.
I've repeatedly repaired my disk and permissions. I do it every time I have to boot. It makes no difference.
At first I thought this was a minor issue I could live with, since I don't reboot my computer every day, but it's become increasingly annoying. On several occasions I've had the computer crash unexpectedly which meant I was out of business for half an hour while I tried to reboot it. Once this happened while I was giving a presentation to a group of people with a projector, which was extremely frustrating. In fact, compared to other Macs I own or have owned in the past, this MacBook Pro crashes a lot more often.
I've found several other posts about this problem. Is there just some fundamental issue with these MacBook Pros? Is Apple aware of it? Will they be able to fix it with an OS update or a firmware update? How long will I have to wait for that?

Apple>About This Mac>More Info>Service
Please read the warranty paperwork that came w/your computer.
You have 14 days to return the computer w/no questions asked. 
You have 90 days of FREE phone tech support on top of your standard 1 year warranty unless you also purchased AppleCare which gives you an additional 2 years of coverage plus FREE phone support.
Strongly suggest that you take FULL advantage of the above before it runs out.  Let Apple deal w/the problems.

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