I dont think this is the case with your son but here is something to consider. My friend has a daugher (oldest of 3, about 5yo) who was VERY hard to wake up, as she'd be grumpy, uncooperative, and VERY whiny. (With 2 younger boys, she had her hands full!) Her daughter was diagnosed with something like... hypersensitivity (not sure exactly... slightly OCD, but not that. )
Between that diagnosis and her daughter's temperament, she learned to do things like this .. drop everything and give her a GOOD back rub, body massage, good strong hugs, etc. She needed the physical stimulation and the attention during her slow-wake up time. IF she did not take that 20 mins or so of full hands-on attention to her daughter, she would pay for it with 2-3 hours of dealing with screaming, whining, meanness to the younger brothers, etc.
I share this because I hope that you can learn to adjust and figure out how to give your son whatever it is he needs. Most likely some touch, soft soothing words, a soft easy pace as he transistions to fully-awake daytime activities...
(I am a slow waker too, I HATE it when my husband flips the lights on and expects me to jump out of bed and be up & at 'em right away! I NEED my snooze alarm 5 days out of 7!)