This is a Yes and No question.
It's a bad idea because you wont be getting the max output and quality from your speakers. Also an aftermarket always has better EQ's and neat little features like a built in SX or Sirus radio tuner (or both). There are sometime 1-3 outputs for amps which makes it simple to hook one up. Where on a Stock there is no outputs so the amp input will be coming from the rear signal. Also most head units have a cd changer that can be used from a 6-disc to a 12-disc.
It's a good idea beacause a decent head unit doesnt cost $100 think more of the $250-$800 range. You can get a really nice pair of speaker with the money saved. Look for speakers with low RMS like 2-40 RMS. Check out the speaker sensitivity to find the most efficient speakers for your vehicle. (For instance, a speaker rated 3 dB higher than another will require half as much power to produce the same output.)
Need more info? Go to the link I provided below from Crutchfield.com they have great info.
What to look for when choosing a speaker/head unit