Recently I ran into a frustrating issue on my new MacBook Pro Retina (with 512MB SSD). The time of (re)boot took a lot of time, holding the screen black for a long time.
I checked several tips, but it was not due to old hardware (...), also not that my disk was full (more than 50% free space).
I searched a lot and found a solution that works actually pretty well and seems really stupid to me (a kind of Microsoft-type-solution-when-something-unexpectedly-stop-working-well).
What you need to do is to go to System Preferences, and selecting Startup Disk. Then, select your primary disk, and hit ‘Restart’ from the same window.
That's all! It worked for me pretty well!
By the way, it seems that this happened after the update of OS X 10.10.3.