Uploading files to iCloud I am essentially looking for a way to upload files from my iPhone that it does not recognize or can handle with the goal of keeping them for later use on my computer.

I see lots of ads for Dropbox, Skydrive, etc, that would let me grab files on my iPhone and keep them safe until I can get to a full computer (especially limited-time-availability files that must be downloaded within a timeframe.)

So my question is, can't I do this directly with iCloud?

I'm dealing mostly with files iOS doesn't understand, like proprietary formats, but there may be some images etc. It goes without saying all files must be stored untouched, without any kind of compression being applied.
On iOS, the short answer is no. There is, unfortunately, no app that allows you to manage the file system, in the manner that you are speaking, in iCloud.