Real Difficulty v. Artificial Difficulty
Difficulty as a philosophical concept could fill volumes and I will not claim to be any kind of expert there, but I will say that generally speaking "difficulty" tends to mean how adverse the rules are in comparison to the player's skill-set. As applied to a jumping puzzle, where the player must complete a series of tests and judgments with a calculable level of precision, the difficulty lies in how complex those tests are and how precise they must be. Throwing additional monkey wrenches, such as a time limit or enemies, increases the difficulty (though they can be thought of as part of the "global" test, that is to say a jumping puzzle with a time limit's test is "Complete X jumping tests in Y time.").
In gaming however I feel that some of those monkey wrenches are more "legitimate" than others. A "legitimate" increase in difficulty places more natural tests on the player's capability; tasks that require the player to complete tests faster or more precisely. Alternatively, "artificial" difficulty are situations that either have little relevance to the player's skill, step back the ease of a player's interface with the game, or otherwise impede progress outside of the test. The artificial ones naturally are those that tend to frustrate and make a task feel tedious, while legitimate difficulty makes success more satisfying.
From the infamous Clock Tower, the legitimate difficulty challenges were the complexity of the jumps and the time-limit. These are both genuine tests of the player's skill and thus I can't really fault them. The jumps included rapid leaps onto sometimes unclear positions, switchbacks, differences in distance...the works. A time-limit strikes me as legitimate perhaps because of tradition, doing something in a fixed time or "faster" than everyone else is practically a time-honored way for people to contest. Furthermore, the rewards for completing this challenge were perhaps the definition of optional in Guild Wars 2: an achievement that was not part of the meta-achievement for the event (though to be fair, this was not initially clear), and a pair of Exotic boots with + magic find and common stats (which could also be obtained doing the other PvE of the event).
Artificial Difficulty (Tedium)
This list is a bit longer because frankly there were plenty of artificial barriers thrown in the player's way that had virtually nothing to do with their ability to complete the task (that is, these factors were not really a matter of personal skill but chance and optimization). Many of these are issues created by intentionally introducing poor game-to-player interfaces. Essentially they remind the player that they are in a game. For the Clock Tower, these included: other players occluding vision, the issues with the camera (often making it hard to see things), the jumps that required the player knew they were coming (leap of faith, the exploding clock face, etc), the minute or so a player had to wait between attempts, lag, and poor collision detection ("I totally made that jump!").
All of these were mentioned by players at some point and I do agree with them, each frustrates the process of success in ways beyond the player's control. You can't really "out skill" the presence of other players blocking your vision. No amount of skill could save a player that jumped towards the clock face without knowing it would soon break. Perhaps you could argue that "skill" can alleviate these but they were choices that were character specific, not player. Furthermore they clearly were not the kinds of skills the Clock Tower, billed as a "jumping puzzle" was intending to test.
Additional examples of what I consider artificial difficulty are: poor camera control (as in the camera is as much your opponent as the enemies), "dumb" units in an RTS (that will stand on a grenade unless ordered off it), and overly complex/confusing controls (that serve no purpose but to limit the player's ability to interface).
No matter what a developer does, players will complain, but I do think one of Arenanet's mistakes in this regard was not properly conveying the players that the Clock Tower was NOT a challenge that everyone was expected or intended to complete. It was posted along with all the other challenges, and while it was referred to as "devious" and would require "nerves of steel and steady feet" the other content of the event was described as "nightmarish" and "macabre" and the terminology fit the general theme of the expansion; giving player's the false assumption that it was meant poetically.
As stated previously, it was not made clear to most players that challenge was not part of the meta-achievement and its reward was obtainable elsewhere. If instead it had been made clear early on that this was a challenge of intense difficulty, it might not have put so many players in the stressful position of trying to complete it lest they miss out on the title and meta achievement.
With any luck, from this Anet learned a few lessons....in various blog posts and media sources they have reflected some of this, but time will tell. I look forward to more honestly, the GW2 Halloween event (IMO) blew WoW's out of the water.