Inconsequenti-AL
Breaks Games
Description changing seems a good way to go... The flaming warrior is a particularly good for fireball - going to steal that. 
Although, IMO, a bit of care is needed - the magic missile example above where the players didn't realise what they were being attacked with. What if that spell killed a PC who didn't know that his Shield spell should stop it? Easy for a DM to miss! Tricky.
Also, what do you do in the case of a counterspell or high 'what's that?' spellcraft check?
I quite agree that the familiarity of many core spells does take away the magic feel... I've recently been running Arcana Unearthed, complete with the alternate magic system. My group and I have found this makes many things new and unfamiliar... although it works in a similar(ish) way to the core stuff. In fact, it's slightly frustrating as I've caught myself wanting to use certain 'plot device' spells (e.g. Geas) and they're no longer there.
As far as plot device magic goes - I've (over?)used human sacrifice and demonic pacts as material components for plot magic. Stops the players dabbling with it! It's separate stuff from regular magic IMC. It's lazy, cliched and after reading this thread I think I need to pick up CoC and Unearthed Arcana...

Although, IMO, a bit of care is needed - the magic missile example above where the players didn't realise what they were being attacked with. What if that spell killed a PC who didn't know that his Shield spell should stop it? Easy for a DM to miss! Tricky.
Also, what do you do in the case of a counterspell or high 'what's that?' spellcraft check?
I quite agree that the familiarity of many core spells does take away the magic feel... I've recently been running Arcana Unearthed, complete with the alternate magic system. My group and I have found this makes many things new and unfamiliar... although it works in a similar(ish) way to the core stuff. In fact, it's slightly frustrating as I've caught myself wanting to use certain 'plot device' spells (e.g. Geas) and they're no longer there.
As far as plot device magic goes - I've (over?)used human sacrifice and demonic pacts as material components for plot magic. Stops the players dabbling with it! It's separate stuff from regular magic IMC. It's lazy, cliched and after reading this thread I think I need to pick up CoC and Unearthed Arcana...