If you can get tickets to the games you want to see through the ballot I would do the tour independently as you will have more flexibility to visit where you want between games. That is what my friends and I did in 2007, and it should be cheaper.
The TGV/train network is great to travel between cities, and you can organise your own accommodation.
Tours like Williment Travel will take a lot of the hassle away so it depends on what you want from the experience. I'll never forget seeing many from their tour group walking around Paris after the QF in their adidas tour kit looking like they wanted to be somewhere else. We all ended up at a bar watching the NPC final live.
It's much better to be incognito. 