2) To expand on that If you really did want to dramatically replace the class then you would use the Injector system (http://doc.silverstripe.org/framework/en/reference/injector). This is however new, and a few parts of the core are not quite updated so you will likely run into issues in the short term but more places are being updated as time allows.
Sorry I haven't got a nice answer for 1, I know you'd need to customize UploadField but at the moment, only way to rename would be in the assets section. If the name is programatic then you could rename the file onBeforeWrite() of the Image object.
For 3 again, I don't think I have a nice answer. AFAIK nested folders in templates (even for categorising template types) is not supported but it did change in 3.0. In theory it should be supported or a pretty simple task in core as there already exists a manifest of templates which could include directories (much like the classmanifest). Would need a few tests and documentation but defiantly a doable enhancement to core if someone wanted to tackle it (or fund development).
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