Heres to hoping we get a TIE for Skyrim soon

Setting encounters and loot to all appear at level 1 up was easy to do and actually was part of the first Oblivion overhaul (M.O.E.)
A few factors to consider for the future. An arbitrary division could be made between two schools of modding toward overhauls. Those that use script extenders and those that use the more traditional adjusting record by record what is to be changed. With OBSE (and to a lesser extent FOSE) each release offered new avenues to changing things. The upside was that with scripts operating compatibility amongst mods that didn't use them was high, but there is the chance that other script extended mods would conflict.
The more traditional route of record by record adjusting of things has the upside of being something that could be tracked with tools (bash & edit) but often meant that other mods that affect leveled lists or other records modified would need patching.
That dividing line is again arbitrary and taken for granted with Oblivion, but Fallout3 with leveled lists mods that make use of script extender made much more extensive use of FOSE to do things like adjust encounter types and adjust weapon stats and the like. moistly due to the late appearance of Wrye Flash
Both tools are on their way (Script Extender and Wrye Bash), so it will be interesting to see what form takes hold as the dominant method for level scaling.
I'd think for planning ahead that having leveled lists adjustments be traditional record by record approaches while having combat, stealth, magic mods be far more script extender driven would be ideal. Bash is still under constant development and making use of the traditional approach has value for compatibility reasons.
So yeah an unleveled/unscaled overhaul like in M.O.E. or TIE with just the lists done would be great. Then the other game settings, combat tweaks and the like done individually from there.