When tiny mountain goats historically won GTs, it was because they achieved something incredible in the mountains because they were truly special climbers - think José Manuel Fuente, Federico Bahamontes, Luís Alberto Herrera, Charly Gaul, Lucien van Impe. GTs have always been won and lost in the mountains? Tell that to José María Jiménez, who lost 13 minutes across the two TTs of the 1999 Vuelta and was under 10 mins down on Jan Ullrich overall. Or Lucho Herrera, whose sole Vuelta win is a pretty small consolation prize considering the amount of time he used to lose in the 200km of TT or so in the Hinault era. The GTs may have always been won and lost in the mountains, but the rest of the course decided who was playing for the win in them.
Personally, I'm not ready to anoint Nairo Quintana a greater climber than Lucho Herrera just yet, but Nairito has already eclipsed his national cycling icon's palmarès. But what we have to recognize is that some of the great exploits of those climbers was caused by the unfavourable parcours. If you don't give the climbers reasons to have deficits, there is no reason for them to take the risks in the mountains. José Manuel Fuente's incredible day-after-day solo escapades in the mountains of the 1974 Giro were the result of him having lost several minutes into Sanremo after miscalculating and not eating enough in a hilly stage. If he hadn't lost that time and held all the cards on Merckx in the mountains, he'd have sat in the bunch and followed wheels and the race would have been infinitely worse. Epic solos like Chiapucci in Sestrières would not have been necessary in the slightest if there hadn't been long time trials, because he would only have needed a few seconds over Indurain rather than several minutes. It can be seen in the "Purito template", the sprint for the seconds at the top of the mountain; it's progressively rarer that we see riders even going from the base like Sastre did in 2008 now, let alone the "several mountains from home" escapades. A situation like the Giro 2010 where the climbers were given a big deficit without that kind of time trial mileage, is a freak occurrence (and nevertheless they included tougher rouleur challenges to balance the parcours another way, by introducing the epic sterrato stage) and can't be relied upon.
A GT should have two TTs of reasonable length. They can be two long ones, a longer and a shorter one, or so on, but there has to be sufficient cause for the one-dimensional climbers to lose time that they are close enough in the GC to feel like they have a chance if they take risks, but not close enough that they don't need to take risks to do so. Look at the Cercedilla stage in the Vuelta - Aru had to pressure Dumoulin from afar because the stage was easy enough that if they didn't attack at that point the climbing was easy enough; the muscular time trial specialist who could climb enough to get by was fighting the lightweight grimpeur who can TT just enough to get by. They made no use of Jito d'Escarandí, a legit ESP climb with comparable stats to Fedaia, until the last 2km; but on something that's really little more than a medium mountain stage (the Sierra de Madrid climbs are often over-categorized) the climber's hand was forced, but only because there was no tomorrow to wait for anymore. The likes of Contador, Froome and Nibali are all-round enough that they would be fine on a more balanced parcours and still competing for the win on the climbs anyway; they just might have more trouble controlling the likes of Quintana that way, and Nairito might not be able to rely on his patented "do a long one in week 3 and stake everything on that one stage" technique either.
An MTT should be an occasional treat. It's a great thing for a warmup race in fairness, but I think it has two main uses - one is in circumstances where logistics dictate a road stage is more difficult to organize (e.g. Kronplatz) and the other is where the climb is of a nature where it maybe would struggle to produce the same kind of time gaps it will in an ITT if they did it in a road stage. Think of the several Sierra Nevada TTs the Vuelta has had; the "traditional" version on the A-395 is long but its gradient is fairly consistent and gradual; nowadays it would be difficult to get away from the trains on until very late on, whereas in a chrono there will be definite gaps. Nevegal is a similar one where the climb isn't especially threatening and the time gaps of the TT are probably more than there would have been in a road stage climbing it. The exception is the Passo di Fedaia, because an MTT there would mean several hours' straight coverage live from the Passo di Fedaia, and it doesn't get better than that.
The other factor that has come from the increasing tailoring of the GTs towards the grimpeurs is that it has greatly devalued the GPM (although admittedly to a great extent Richard Virenque is to blame as well). The best climbers don't target it because unlike in the days of Herrera, they have no reason to think they shouldn't be contending for the win and they aren't eliminated from contention in the rouleur part of the race; the classification has as a result become a breakaway's plaything, except in the Tour where they've revamped the classification which is now massively biased in favour of HC climbs and MTFs and as a result has become a consolation prize that GC competitors can pick up as a consolation prize; Froome even won it almost accidentally last year.
I want to see the great climbers duelling as much as anybody. I'm known as a huge grimpeur fetishist and almost all my favourite historical riders were pure climbers. But as much as I want to see them fighting for the win, I also want to see the true battle that is one man against the mountains, which is part of the romance of the sport. And we aren't going to see that on courses where even the most one-dimensional climber need not waste any energy until the last 5km.