On Mods
I’m still planning a “guide to the item modification system” post, once I sort out the tangle of the flip-flopping mods changes in the last few beta builds. In the meantime, though, check out On mods: the building, salvaging, and picking thereof from Stop over at The Stoppable Force. It’s a great post and gives a good overview of the principles of the system rather than the specifics.

From my limited experience with the weekend beta, I don’t really see how the mod system will let you use your favorite armor look successfully at higher levels.
Even with the mod system, it looked to me that the majority of stats were baked into the item, meaning that it would be pointless (stats-wise) to mod a lower level item instead of a higher level item (by quite a lot).
I’m hoping that it works out ok at max level, but I suspect it won’t be acceptable to the “serious biz” crowd.
I have a mods post in the works (and I’m hoping to get it up today) but in short – I believe a lot of gear in the live build will have a lot of mod slots open, so stats will be dependent on mods rather than baked in. Social gear works this way, as does a bunch of craftable gear. Even stats like weapon DPS and armor rating are affected by mods – so hopefully fully-moddable gear should be competitive with more traditional stats-baked-in gear.
The penultimate weekend test build had a ton of armor schematics (all available as bonus loot from Underworld Trading missions – not sure if they were dropped as well) that were basically nothing but mod slots. Looking over the patch notes for the final beta build, it looks like they added a lot more schematics to that list. I think they’re pretty serious about fully moddable gear.