People use the difficulty of bike racing as a convenient excuse for easy routes and conservative racing, but it has little to no actual bearing on why there's such a history of doping in the sport (which there is, and I don't think this is a statement that belongs in the Clinic, we're not discussing the actual ins and outs of doping and who is at it, just acknowledging that the sport has a history of it). People cheat to run 100m in a straight line.
Sports science, both legitimate and Clinic-related, has improved massively over the years, so using "it's too hard for people to do without cheating" as an excuse for dumbing down is organizers and race designers trying to justify their own lack of imagination. The 2009 Vuelta was very conservatively raced. Was it because it was too hard? No, it was because they paced the mountain stages all wrong, so riders were afraid of losing time on the steep MTF at La Pandera, meaning they soft-pedalled the much better-designed Velefique stage so as not to be tired for it. The 2009 Tour was very conservatively raced. Was it because it was too hard? No, it was one of the worst TDF designs of all time. It was raced that way because one team was stupendously dominant and would have controlled the race easily no matter what route you put there.
Shall we have a look at the stages that have produced the best stages of recent GTs? Yes, there are some short ones in there, but there are also some very decidedly NOT short ones. Yes, there's Formigal in the 2016 Vuelta, Semnoz in the 2013 Tour, Andalo in the 2016 Giro and Alpe d'Huez in the 2011 Tour, but many of these were created by circumstance. Semnoz and Alpe d'Huez were the last chance for the climbers, so they weren't the product of the short stage so much as desperation to make the bid for victory (same for Nairo's unsuccessful attack in the 2015 Tour); after all, Cercedilla in the 2015 Vuelta was great for the same reason, but was a full length stage, just as with Sestrières in the 2005 Giro with the epic introduction of Finestre. Similarly, ending with a big mountain will work if the best climber left in the race has a deficit (Bola del Mundo 2010, for example), but if they already lead, it's often just a damp squib (Zoncolan 2014, Mont Ventoux 2009, even Tonale in the beloved 2010 Giro, as it paid the price for the amazing Aprica stage the day before). Here, Angliru 2013 is almost the outlier although that can't really be considered a "short stage" either, though it's far from a big long-distance mountain stage.
Outside of these situations, however, there is little to suggest that these short stages are significantly better at the pro level (the jury's still out on this at the espoir level at Avenir etc. - the last stage of l'Avenir this year was shorter than a women's semitappe though). The Sestri Levante stage of the 2015 Giro is one of the few examples of this approach working outside of week 3 of a GT, where the GC gaps are already well-set and the legs are already well-worn - for it is that that is why they have worked, and if all the stages drop in length, then they cease to have any value because riders don't see them as any better a chance for racing than any other stage, and riders' legs aren't tired enough for them to have that impact. The short stages work best in conjunction with other stages. The Alpe d'Huez stage in 2011 does not work without the Galibier stage the previous day; put those stages the other way around and nobody GC-relevant lifts a finger until Bourg d'Oisans. The Formigal stage wouldn't have worked without the Aubisque stage, because Froome's domestiques wouldn't have wilted around him without having had to work the previous day over four cat.1 and ESP mountains, so Movistar and Tinkoff would have desisted and it would have been a 4km shootout on the steepest part of the final climb. In fact, one of the best mountain stages we've seen where the GC wasn't immediately on the line like in these short stages was 230km with five major mountains.
Without the long, difficult stages, these short fast hard stages don't have the same value. Very little to do with the Clinic, and everything to do with route pacing and the situation on the GC leading into it.