I don't read it that way. To me it seems like a typical "Wizard" would get spells per day, but he could also spend a feat to get an at-will or per-encounter magical ability. These abilities would not be called "spells," since "spell" would only refer to per-day magical abilities.
Personally, one design aesthetic I'd like to see is inspired by Magic: the Gathering. Namely, you have to gather your mana to cast your spells. Maybe you have X mana per day, and you spend 1 mana whenever you cast a spell, or possibly 2 mana to do a really powerful version.
Then you'd have an ability, Draw Mana, which would let you spend a standard action to gain 1 mana, but you'd have to spend it within 5 minutes or else it would fade away.
To keep this from being boring (i.e., you only cast a spell every other turn), maybe the act of drawing mana makes you imposing like Gandalf when he intimidates Bilbo early in Fellowship, causing creatures nearby you to take a penalty to attack rolls for a turn. Or maybe a fire mage who draws mana could deal minor fire damage in a close burst, as fire swirls around him dramatically. Different types of wizards would have different minor effects that occur when they draw mana.
So you still have spells as a per-day resource, and if you use all your normal allotment of spells you can no longer just snap your fingers and cast; you can only cast every other round.