I played a spellcaster in a short lived campaign. IIRC, my 1st level spells were cure light wounds and magic missile. I stuck with will as the good save, though did play with selecting reflex as the good save.
I can see some potential for abuse if you use PRCs in the campaign. Some PRCs need specific ranks in skills and some require a certain base save amount. With the flexibility in choosing skills and saves, you could have folks entering PRCs sooner than you might normally expect.
If I was DMing that I wouldn't have a problem with it, but you might.