How exactly is the skill system worse? I think the skill system in Diablo3 is pretty amazing. Instead of putting 1 point in a skill until you hit level 30 and dumping everything. In fact Diablo2's skill system was pretty retarded.
This has been discussed over and over. But because you asked -
Diablo 2's 'put 1 in every prerequisite till you're ready to specialize' was indeed flawed because it resulted in degenerate gameplay through the early levels, but the overall idea behind the system - specialization & progressive upgrades for every single skill - gave you fine grain control over a character's abilities and increased replayability by offering a different playthrough experience for each 'build.' Besides which, the fundamental flaw in Diablo 2's system was easily fixed by allowing players one respec per character, which solves the gameplay degeneracy entirely.
Of course, because the progressive upgrades for skills were not equally useful - and at times were completely retarded - eventually people figured out optimal cookie cutter builds that reduced the fine grained customization to the equivalent of picking one of several subclasses for each macro class - ie zoomancer, cold sorc, lightning sorc, hammerdin, zealodin, etc. But even with the creativity being squeezed out of the system by accumulated game knowledge, you STILL got the benefit of the replayability because of the need to build multiple characters, each with different advantages and disadvantages, suited for different tasks - ie trash farming, Meph. farming, Baal farming, uber farming, elite farming, PvP, etc, and you STILL got the benefit of having every skill in the game scaling with the amount of specialization, leading to personalized builds that employed a cookie cutter core with an individual choice of optional skills.
By contrast, in Diablo 3, every class receives the benefit of infinite respecs at every stage of the game and the skill system is such that the bulk of the skills in the game only scale in one direction. The result is two-fold. First, nobody ever makes a second character from a class: the amount of replayability in the game is therefore reduced to N, where N is the amount of classes. Indeed, it is reduced to less because the balance in Diablo 3 is such that every class is capable of doing virtually everything useful that you want it to do, with the advantages / disadvantages being minimized by design, and because of the Paragon system they introduced you are discouraged from switching characters to begin with. This is the classic 'rail roading' design principle that Blizzard West has operated from WoW onward.
Second, while you do still have the option of switching skill sets and gear around to produce unique play experiences at 60, because skills are designed to scale in the same direction - instead of uniquely for each skill - and because Diablo 3's skills are just overall less different, there is far less variety than the skill system at first glance gives you. For example, using frogs vs. using spiders vs. using skulls as a WD is practically a moot cosmetic choice - the play style difference between them is minimal because they all do the same thing and upgrade the same way. Thus, while min/maxers are still going to tell you to use X because it's a few % better than Y, switching to the use of X over Y introduces very little novelty to your game.
By contrast, using, say, poison nova vs. bone spirit was a night and day decision in Diablo 2 for a necromancer because not only did the two skills result in very different play styles, but they led to very different advantages / disadvantages vs. the various immunities in the game. Of course, a defender of Diablo 3 is able to make the argument that there are equally important choices in Diablo 3 - for example using bears vs. using sacrifice. But the proportion of skills falling into the cosmetic range vs. the night and day range is greater in Diablo 3, both because a lot of Diablo 3's skills lack variety / balance, and because Diablo 2's skill system had progressive upgrades for every skill - allowing you to individually customize the way each skill scaled up - while Diablo 3's skill system is designed to have blanket scaling and so forces the skills into a specific design template.
The importance of build decisions in Diablo 2 was thus greater than that of Diablo 3 at both the level of replayability and actual play style. The final result is that there was a longer period of time in which players were kept in the loop of novel experiences, and in which they were incentivized to develop new characters and twinks. This is not to say that the skill system is the only culprit, because skill systems do not exist in a vacuum and it's the holistic effects of its interaction with the rest of the game that produce overall player experiences. Thus, an evaluation of the skill system by itself is worthless, but becomes useful when you start looking at how it interacts with the rest of the game to produce novel experiences and replayability incentives.
