The pacing was the biggest problem tbh; in both batches of mountains, they had the steepest finish last (Xorret del Catí and La Pandera), and fear of those induced conservative racing in the races beforehand.I guess my was that because of those soft MTFs the steeper non-MTFs thus played a more prominent role in the race..?
Geography prevented it, but doing the 12-13-14 mountain grouping in reverse would have been so much better for the race. Doing the La Ragua-Blancares-Sierra Nevada combo (via Monachíl and Las Sabinas for the first time) would have been stronger in that respect - however it's best as the middle stage because the action was always going to only be on the last climb there since Blancares is so gradual and it pushes La Ragua so far from the finish, but it would guarantee a strong break over La Ragua being an HC climb straight from the off. Stage 12 with the grinder MTF to Velefique after a prior ascent of the same climb with Cálar Alto in between would have been much better as the last stage of the mountain trifecta, with the connectivity of the climbs (would have been better to do the Tijola side rather than Serón of Cálar Alto too) being better for attacking before the last climb.
As it was, the gradients of Velefique were too shallow to create significant gaps when, with two consecutive mountain stages to follow, the GC men were conservative on it, and then Sierra Nevada saw Sánchez drop and Evans mechanical, but again nobody wanted to risk too much with La Pandera the following day, but that stage was functionally Unipuerto and although Valverde was dropped and had a strong fightback, probably the most memorable thing in the stage was the bunch urgently trying to stop Cunego (who had won on Aitana and been around 7th or 8th on GC before the Sierra Nevada stage) from getting in the break, only to realise he'd sat in the bus the previous day and slow to a crawl to let the break form. And that he won that stage and immediately DNFed the race to focus on training for Mendrisio.
Xorret del Catí and Aitana could have potentially been swapped around, the stages wouldn't even have needed that much amending. I think the decision to put them the way around they were was based on Aitana being HCish (it's a bit of a stretch but just about merits it) and XDC being short and a fairly generous cat.1 - but based on steepness it would have been better the other way around, as the difficulty of XDC forces - albeit small - time gaps, and then Aitana can generate a bit more with more tired legs and making it harder to tempo climb.
Likewise, stages 19 (the multi-col stage around the Sierra de Guadarrama with a descent finish) and stage 20 (a mid-length ITT around Toledo) could easily have been done the other way around and that would have had a big benefit for the mountain stage, as it was I think most people were happy enough with the status quo after Gesink crashed and was distanced. Samuel Sánchez attacked at the start of the descent from Navacerrada but couldn't gap Valverde, Evans chased back to them, but in the end the impetus was lost so much that they actually allowed both Basso and Mosquera to catch back on on the descent.
As a result, I think the deepest flaws in the 2009 Vuelta (the very bland first week, the pacing of the mountain trifecta in Andalucía) were things that not much could have been done about (a better run in to Liège in stage 4 excepted - a hillier route would be ideal to set a bit of a GC banana skin rather than a prologue and a bunch of flat stages out of the overseas start; but failing that, just a safer route with less road furniture and crashing would have been better, this would have given us a healthy Horner and Tondó to add to the GC mix; Horner crashed out of the race, Tondó struggled on for another week but dropped out in week 2), but just swapping a couple of stages' positions in the order without even altering the route (stages 8 and 9, stages 19 and 20) would have massively improved the race.