My desire for a file manager is to 'know' or at least be able to find out where some app puts my files or where I need to put them for said app to see them. Otherwise the 'cloud' seems more like a 'fog' to me. And yeah, I'm new to Apple but not to computing.
In addition, like another poster, I would like to delete specific files and/or keep certain groupings (that "I" determine) together.
BTW I am familiar with Android (got a Droid phone & a rooted {that's jaibroken to y'all} NookColor ereader that is also a pretty good Android tablet). However I really like much of my iPad's capabilities. I'm one of those people who're never quite satisified. No matter how perfect a product is, I want more.
Well, if you want the kind of flexibility you mention your only option is to jailbreak your device. This will give you unrestricted access to the entire filesystem, and you can use an app such as iFile to manage the whole disk.
You simply cannot get apps to operate outside of the sandbox environment of iOS without a jailbreak.
Head over to the hacking section and start reading the stickies in there...