Recall, the Tour used the national teams format off and on through its history until 1968. As recently as 2007 ASO were said to be reconsidering the idea. National teams are just as they sound: like the worlds, you invite the national teams of qualified nations. Unlike the worlds, you don't get one team from every country you can think of; in the case of bigger countries, you might issue invites for two or three teams. Obviously France would get multiple invites, and cases could be made for Australia, Spain, Italy and the Netherlands. Belgium... maybe. So what would using national teams do for the GC? I can think of a few effects.
* Cohesion would be hard to come by. Even if teams established an accepted order, the nuts and bolts of working together would be a work in progress.
* National teams would have to create more organization than they typically do. The Worlds and the Olympics encompass a handful of one-day events, not a three-week stage race. Budgets would have to expand in ways that aren't easy to do. Maybe the national teams could tap into the trade team budgets since they'd be doing their job for them in some respects -- leading Contador to yellow would be a huge boon to the Astana guys sitting at home on vacation. Obviously this would be a massive food fight.
* Some countries would have an easier time than others. Sky is practically a national team already. Astana, BMC and Rabobank too, sorta. Some countries would consist of minor consolidations, like the US (Garmin and the Shack) and Belgium (Quick Step and Lotto). Italy, Spain, Germany and Australia would have their work cut out. Norway would have to pick a sprinter. Sweden and Denmark would be quietly forming alliances. Maybe Canada and Ireland could form a commonwealth team with the odd New Zealander and South African.
And how would it all pan out? I'd love to hear your guesses, but mine would start off thusly:
GC: Spain, Italy, US would be the top tier. Depending on when this happened and how far along guys like Kreuziger and Gesink were, you could maybe bump the US (which is about to retire its frontline GC squad).
Points: Norway! Imagine Thor and Edvald working together?
Team Classification: Spain. Hands down.
Combativity award: France. Hands down.