More but smaller teams.
More variety in stage profiles
Bring back bonusses on intermediates and all finishes.
At least a few shorter mountain stages.
25 KM rule on major crashes during flat stages. yes, keeping upright is important, but now people are being shredded where they absolutely couldn't avoid it. Worse, it kills the competition.
Controversial ideas (not sure if they would be good ideas):
Time differences are decided on the ten km flag during flat stages. Escapees with the last ten km do get the time bonus, but it gives the GC riders a chance to bow out.
No time differences during the last 25 km of a flat stage, but give time bonusses for the first ten finishers.
Variations on this them.
Shredded riders can be brought paced by car, tour-doctors decision. Only used in clearly disastrous cases. The motivation is that we pause most sports to allow for injury treatment. Neutralizing is not practical, so let's pace riders who truly are grated cheese. This also allows decent wound treatment and new clothes. It's a disgrace that we see riders riding around bleeding with completely disfunctional clothing. And no, I'm not puritanical.
Things I (strongly) disagree with the others:
Keep the yellow helmets (you guys have no sense of history!)
Vary Mountainuous and TT oriented TdF's. There's nothing worng with (long) TT's. Why play favouritism on the climbers?

Don't focus on those so called super-climbs. Why play favouritism on the climbers?
Related: This TdF might become extremely exciting due to the fact that the mountain stages aren't crazy. During the Lance years one less mountain stage and one more longish TT might have made the LA-JU contest a lot more Interesting. More mountains doesn't mean more excitement
