Whatever you want to believe, you'll find enough arguments to justify it
Take Wiggins' statement, you can interpret it both ways- either he's right or he's just justifying that despite what he was saying back in 2007, he became a legitimate GC contender. Same with Voeckler coming 4th, either it means cycling is cleaning up or Europcar riders catching up. Generally I think that people got overexcited after the Tour, painting Evans as squeaky clean, the race as very believable blah blah blah. Evans' myth always bugged me- don't care much if he's clean or dirty but he always rode for dirty teams and him underachieving until Mendrisio win can hardly be justified by being less doped. For example, in 2007 he was 23 seconds off Contador (don't remember but it was about 3 seconds without bonuses). The same people consider Contador one of the worst dopers, something doesn't add up (unless Evans is way more talented which is... unlikely). And as for the Tour in general, well. Everyone except Evans and Schlecks everyone was either unlucky, injured or forced to abandoned. Schlecks mostly looked at Contador and showed others to pull and frankly Cadel had no reason to be aggresive; I'd wait for the race with more healthy, rested contenders to look at speeds and judge. Unfortunately, the whole talk about doping is so biased and selective and our own perceptions of the race too misleading, it's quite dangerous to draw conclusions- and probably not worth it.
As for shorter stages, I also didn't agree in the other thread but again- fresh legs may actually make races less exciting. You won't get big time differences, spectacular bonks and maybe you won't even get many attacks because what's the use if you can't really drop anyone because your rivals are super fresh and fit. Take Voeckler again- he can actually climb with the best if he goes all out, only he'll pay for it later during the race. If the stages were short and easier he'd probably simply recover, just like all the other guys who can climb a bit but aren't the best- and we'd maybe get uphill sprints over and over again. It's what's special about GTs, by the 3rd week people get exhausted and only those who are best suited to such races are left- have it any other way and you'll get all the farcical results with TTists hanging on, breakaway guys not giving away the jersey etc.
Also keep in mind that if the stage isn't tough and long enough (and especially if it's like this throughout the race), on the last climb or two leaders will still have plenty of domestiques. It just happened that in this Tour those mountain domestiques weren't very effective but imagine Basso having a super fit Szmyd to set the pace. Szmyd's tempo would be so fast, no one would be able to attack- but also no one important would be dropped because everyone would have reserves.
Alpe d'Huez was great but it could have easily been a borefest until Alpe, if Contador didn't decide to have fun (or decided stage wins is his priority and only went on the Alpe). No one would attack on Telegraphe and it would be a pretty regular mountain stage, seen from the beginning or not. And the stage which finished on Galibier was also very good and very hard- and we got to see all 3 major climbs. And if it was any easier it wouldn't have caused the likes of Contador and Sanchez troubles.
Giro is actually the argument FOR very hard routes, it usually provides more excitement than the Tour and it's because of long stages with harder climbs (than you see in France). This year Contador overshadowed it a bit because he didn't have any bad days but take him away and you'll see how unpredictable it becomes. On the first mountain stages differences are more modest- except AC only Rujano (who lost 6 minutes on dirt roads) gained any substantial time on Etna (but also Scarponi lost some time). But if you have a weekend with 3 MTFs in 3 days- like Grossglockner, Zoncolan and Gardeccia- you see plenty of attacks, big differences and major GC shake-ups. Everyone has bad and good days, you see Scarponi and Nibali taking turns outclimbing each other, Rujano seeming to be on his way to the podium and all of sudden cracking on Zoncolan, Anton once being on the podium and the day after disappearing 50 kms from the finish... It's the case of how they manage their energy but it doesn't mean no attacks- Nibali probably knew that the stage to Gardeccia suits Scarponi more so it made sense to not save himself on Zoncolan etc. (If it's even possible to save yourself on Zonco- probably not.) And sure as hell you don't see riders who aren't awesome climbers on the top of GC. Surely some riders will always save themselves for last mountain stages, last climbs and so on, and try to win GTs with one attack- but routes don't have much to do with it.
As for it encouraging doping. Well, back when it was a lot less effective, stages were longer and done with worse equipment. They could do without hardcore doping if they wanted. (Especially that if they were all clean they'd go significantly slower.)