I am assuming you are weighing the performance of the S v. the Glass top and updates of the 03.
I think it depends what you see yourself using the Boxster for.
My understanding is that everyone likes the updates of the 03, and there are supposedly a lot of the same bits that went to the Base from the S so these are even closer than you might think.
Even though I live in a (sometimes) colder climate, I went for the simplicity of the early boxster myself.
Drive both before you decide. I just bought my 2000 S after test-driving several years/models. The performance of the Base just didn't move me as much (so to speak). But if the '03 is enough fun for you, it's a great choice.