Spellcraft - Identify a spell as it is being cast. "Controlling" spells when casting them yourself.
Knowledge (arcana) - Identify a spell already cast by material components/foci still in place. Identify material components/foci needed for a specific spell. Research new spells. Also may be thought of as Knowledge (magic history).
IOW - Spellcraft is "experimental work" and is the stuff you do "on the fly" while Knowledge (arcana) is the "theory work" and is the stuff you do "in the classroom."
This also explains (to me) why you have to make Spellcraft checks for Epic Spells - no amount of intellectual knowledge prepares you for the difficulty/strain of throwing these "in reality."
I use both as well. In fact I expanded upon them for my spell creation and research rules. Knowledge Arcana is used to get to research the spell and assign the parameters of the spell. Then Spellcraft fintunes it and assigns the material companents and level.
I look at it this way- the main people arcane casters to center around this knowldge and craft of magic is the wizard. The wizard has a high int- so they are making up the skill points there.
Are all wizards going to be as studious? No, some wizards are not interested in the how, why, or what of magic- but in the power that exists. Those wizards would not put skill points there.
Do other classes have this kind of situation?
The only two I can think of is appraise and knowledge (jewelry) for a rogue.