I have a feeling this is going to be like copy/paste or MMS on the iPhone. Something that SHOULD have been there from day one but ended up not being integrated until updates much later.
I think the iPad will reveal its true potential once we really start to explore the practice of cloud-based personal computing. Being able to seamlessly explore your media on your computer, throwing it over onto the HD bigscreen with your Apple TV (also a long bet but may prove its place after some revision), or taking it with you on your iPad.
Having access to your media in high quality wherever you go, THAT is where it's at. The USER needs a file system for their personal content, but not inherently to access all the deep, dark hallways of the OS and file structure like on a desktop. I'd bet that Apple will bring a solution to the table after the iPhone OS4 comes out and brings an iPad update thereafter that will involve accessing your files remotely and bringing multi-tasking and the ability to flow media or data from one app into another.
These are valid concerns but I have faith that they'll be addressed; maybe later than we'd like. One thing is for sure, this device is going to be hard to compete with from PR alone regardless of how it does. The other device makers are chronically characterized as "me too" players. The App store obliterates the old PC pitch of having a large body of software available.
Like the iPhone, I was equally excited about the product and skeptical of its ability to succeed. From right this moment, it looks like they may have pulled off that magic of building/revolutionizing a market all over again. However you feel about them, they sure are doing some things right.