I've been grappling with this too...
I currently run a Time Capsule as a NAS for Macs and PCs, and wifi access point for all my wifi devices (ATV2, iPhones, printer, blu-ray player, wii, etc). in my home, which I back up with an external My Book periodically. I can even access the Time Capsule remotely from my MacBook Pro using afp and a pre-assigned host name (via DynDNS.com). I also use the Time Capsule to store our multiple iTunes libraries that we share via Home Sharing.
I am a happy customer with all of this, but I have two gripes with the Time Capsule:
1. No remote ftp access i.e. no remote access from a windows computer.
2. No iTunes server. I cannot run iTunes from the Time Capsule. Therefore, ATV2 has to go through a computer running iTunes, in order to access media stored in the Time Capsule.
I've been contemplating replacing my Time Capsule as a NAS with a Mac Mini and external drive attached via Firewire 800. Will this resolve those two issues, if I do? Please explain. Thanks in advance!