Depends. If the characters have a certain minimum amount of info on the world around them, then no problem. Using the standard scheme from the MM is an easy way to duplicate this character knowledge without burdening the players with a ton of minutia.
If, however, I'm running a campaign where the players know very little about the world (say a Gamma World campaign, or a planar campaign), then changing the stereotypes is an easy way to limit character knowledge. It can also be a lot of fun for both the players and the GM, as the unknown heightens tension and adds drama.
Regardless of the type of campaign, I see this as a matter of degree, not either-or. I may change many creatures, or very few, but I'll never change none or all.