Couldn't this be some kind of an inherent problem, if the funds can't be spent before some number of confirmations, even if the change goes back to the same address? Doesn't this lock up the coins unnecessarily?
It's generally safe to spend change after 1 confirmation. If your wallet doesn't allow this, then that's a limitation of the wallet you've chosen to use and not a limitation of the bitcoin protocol.
Is it an inherent problem? Perhaps. In the same way that flammability is an inherent problem of paper currency. It's an attribute of the design that users need to be aware of and take the necessary precautions.
Don't get your paper currency too close to fire. Don't store all of your bitcoins in a single output if you want to be able to spend portions of it faster than one transaction per 10 minutes.