So this is my vision.

You get a GUI interface. You select a .deb, set whether it should be installed straight away with Hildon App. Mgr., or whether you want just a Fremantle-compatible .deb (e.g. to install it with dpkg).
Beside this, you select whether you want to download exact differences or use the built-in algorithm which should work in most cases.

The modified debs will have the icons in the right places and .desktop files (icons in the menu) already fixed.
The .desktop files will be fixed too. They'll have a forced rotation workaround already applied (X-CSSU-Force-Landscape=true) and executables will be launched via meecolay.

Users will be able to send me the "diffs" between original and wanted versions so that they are included in the MeeCoLay database.

There'll be a command line interface, hopefully.