Here are my suggestions:
Attacking in the mountains has greatly decreased over the last 20 years. What we have now are a pack of GC riders riding along, whittling each other down to a small group, until someone attacks in the last 5km or so. This is mostly due to advancement in training, equipment, radio, and doping. These things allow riders to conserve energy like never before, and attack only at the very end, or when the team director tells them over the radio. The race has much less to do with strategy, or guile, and more to do with control and attrition. Thus these changes are in order:
• Limit teams to 7 riders - This will make it harder for teams to control the race.
• Limit race radio - either to riders getting info from officials, or no splits allowed to team cars, or riders. Or only one way from riders to team cars. Or just eliminate them. Having the director know time splits and where everyone is on the road is the big problem.
• Consider not letting the team car on some stages, or sections, such as a final climb - riders only getting neutral support with mechanicals.
• Many more stages with uphill finishes. Riders are faster, domestiques are more specialized, bikes and gear are lighter, training is better, riders prep more for one race, and the drugs are better. Some people scoff at climbs like Angliru and Zoncolon, but even last year we didn't see gigantic splits on Angliru, and this year's climb up the very steep Xorret de Cati in the Vuelta, or the "brutal" back-to-back-to-back mountain top finishes did no where near the damage expected. Riders are faster, so we need bigger, tougher, more frequent mountains. A Tour should have 10-12 mountain stages, with 8 or 9 of them mountain top finishes. At least one of these days should be over 5,000m of climbing.
Making the GTs easier has not quelled doping, as some suggested it might. So drop this silly notion. Making them easier will insure we'll have the top 50 riders riding to the last 10k of every stage together. If you're worried about my above tough stages, scatter them with rest days, or spread them out more.
• Have at least one col go over dirt. They did it in the old days, and in the Giro a couple of times, they can do it here.
• Have some years go through northern France, and over some cobbles. They used to do this a lot in the past, but only in 2004 did they try it again.
• Bring back the Puy du Dome! Not much room at the top, but it has been raced before, and could be again.
• Consider large time bonuses (1 minute) given at intermediate sprint points, and KOM cols.
• A bigger variety of ITT's, including downhill ITT's. Though not pure downhill off a big col. Too dangerous.
• TTTs that go over a mountain pass. Some right away, then have another flat 20km to the finish.
More general sport ideas:
• Institute the CO blood doping test. More aggressive random testing during the race. Stricter penalties for missed tests or delaying officials.
• Flex the doping sanctions. If your values are suspicious, you get a one-month ban. Test + and cooperate, 1 year. Test + and don't cooperate, 2 years. Test + and hire Floyd Landis legal team, lifetime ban.
• Work with convicted dopers to help clean up the sport, and to help break the omerta, and stop stripping them of past wins other than from which they were caught. Along these lines, educate younger riders towards doping.
• Flush the UCI as is, and set-it up as an independent organization. Put someone like Sylvia Shenk at the helm, or Greg Lemond.
I don't see salary caps working. The money would have to be pooled, with sponsors thus spending their money not on their team, but on the sport, or events, and they may not want that. However, and this may be a big point buried in a paragraph here, there is great potential here to not put so much pressure on riders to perform at all costs, which could help cut into doping.
I like the idea of everyone on the TTT having to cross (except maybe one rider, due to injury or mechanical).
I don't care for adding more jerseys.
Cut-off time changes aren't needed. My above plan of more climbing will cause enough attrition as is.
Replacing riders on a team is not practical.
The Tourmalet has no room at the top for a finish line. They could however go over it, and finish at La Mongie, instead of dropping all the way to the bottom. This idea would be a great one.