To be fair to GEOX, the rules did change between them setting up the team and the licences being given out.
But the whole thing is that we need to give the organisers MORE flexibility, not LESS. When you fix over 80% of the team entrants as rigid, then the organisers have to fill that extra 15-20% with what serves them best.
Remember that the Tour de France is a business. They need to make money. They need the fans lining the streets and they need the sales of TV rights; if there aren't as many fans, the event doesn't look as good, they don't make as much money. Now, a lot of people are die-hard cycling fans and will go and watch the race regardless. But there are a lot of casual fans in small towns and villages in France who don't really follow cycling, but have a passing interest. The organisers also know that one of the main things they have to sell the audience on is France - the towns and regions pay to have the Tour because it's good promotion for the area. Having local heroes who will be riding through their hometowns is good because it gets fans out onto the streets to cheer on their boy (see all the painting on the streets for David LeLay in the first three stages of the 2008 Tour), and keep the French atmosphere (which is already far more diluted than the national feel of the Giro and Vuelta) that promotes the country as a whole. The Tour has been getting increasingly less and less French in recent years, and the ASO are keen that their more local, less global sponsors and contributors get their money's worth too.