On ITTs, I reckon a template would be something along the lines of:
1 short prologue ITT
one of mid-decent length (30-40km)
one long, challenging one (50-60km).
One in each week. You can vary it; you can replace the prologue with a mountain TT, but in that case you need the shorter of the two normal ITTs to come partway through the first week, placed like the Cholet TT in the 2008 Tour.
Now, obviously this is nothing more than a template; there should always be some variety in race routes; but there should always be enough ITT to give the climbers something they need to take back, and enough mountains to make them feel they have a chance... as long as they attack. Recent race routes have either had far too much ITT for the meagre mountain stages, or had far too little ITT mileage, meaning riders don't have too much in the way of gaps to make up, leading to defensive racing in the mountains. What has been the most exciting GT of recent years? The 2010 Giro. Where the big guns had time to make up so had to make the race exciting from some way out several times. We can't rely on the heads of state to have a collective brainfart and give a decent break more than 10 minutes every time, so another way to create those deficits has to be found.
Another thing that has to be done is to spread the decisive stages out. With totally backloaded routes, all that happens is everybody tries to time their form for week 3, and therefore everybody is not at 100% early on in the race and looking to limit their losses ahead of that final week that they're targeting for form, so racing is more conservative. Again, look at the 2010 Giro: Evans and Vino were already in form coming to the Giro, because they had been at peak form for the Ardennes. Therefore they had to make their time up early, because they might struggle (and indeed did) to hold form all the way to the end of the race, where riders like Basso and Scarponi were hitting peak form. Furthermore, you have to give these riders a reason for being in form early in the race - I'm not advocating you put the hardest MTF of the race on stage 4 like the 2007 Vuelta, or even that you use mountain stages at all to this end - but as long as all of the toughest stages are placed in one part of the route's chronology, everybody with GC ambitions will look to the same point in time. It can be with rouleur stages (eg La Grande Motte in the 2009 Tour, Arenberg in the 2010 or even Middelburg in the 2010 Giro, though with the road furniture that may have been a bit too risky from a safety point of view), puncheur stages (Mur-de-Bretagne in the 2011 Tour, Valdepeñas de Jaén in the 2010 & 11 Vueltas, Agrigento in the 2008 Giro), combinations of the above (Montalcino in the 2010 Giro), 'easy' climbing stages that weed out the contenders from the pretenders without creating big gaps (Alpe di Siusi in the 2009 Giro, Aitana in the 2009 Vuelta, less so Sierra Nevada in the 2011 Vuelta - that's an example of one that was TOO easy) or ITTs of varying lengths (Cholet in the 2008 Tour, Ciudad Real in the 2008 Vuelta). Preferably have at least one of each in the first half of the race to blend up the GC, and not leave it all as a final week sprint - a Grand Tour lasts for three weeks, and you should be racing for three weeks. Leave things for the Tadeses as well as the Gebreselassies.. But there has to be something that sets the GC mix early on. Not just for the spectacle, but for safety reasons - one of the problems in the 2011 Tour was that, as the GC mix was still wide open due to a lack of selective stages in the first half of the race, nearly every team was still up the front trying to protect goals; no reappraisal of goals had taken place, and the péloton was a nervous place for it.