I would say that Legendary Pokemon are harder to raise so that they must be trained extensively before they can be used effectively, so that you don't have a super powerful Pokemon by just training it for 30 minutes. Legendaries are thought to be more powerful than regular Pokemon, and thus need more training to use that power to it's fullest extent.
Because they are not meant to be easy to raise. They are powerful Pokemon, so if you want to raise one, you better be ready to put in work.
To get to from level 1 to level 100, you need 1,250,000 Exp points.