Really, the big difference here is the amount of skills you get at certain stages in each game. In Prophecies, you only get a small handful of skills, which you don't have to buy since you get them as rewards, which also allow you to try certain builds you otherwise wouldn't had you had all skills to choose from. This pretty much forces you to 'diversify' your technique and causes you to play certain ways based on your limited skill options. As the game progresses, you get a wider and wider selection of skills, but at a slow pace, allowing you to try out different builds leisurely and freely. This can be too slow and in some cases, boring for some people.
In Factions, they tried to emulate that feeling of diversity and freedom right from the beginning with the handout of various useful skills. This time, the amount of time it took to learn your character was very short and dropped you right into Kaineng Center with just about every skill to choose from at your fingertips. For some, this can be a sense of overload, which causes you to just find the most useful (or 'best') skills that fit your play style. When you do that, you tend to no longer feel like changing up any skills, or trying out other builds because you 'already have the best there is'.
Not saying one way is any better than the other, just different. Although I tend to be in the latter boat, agreeing with many of you here. I went through Factions with my Ritualist, and briefly tried out some Channeling skills (the ones I, personally thought were the best), then tried a healing Rit (again, just buying the few skills I liked), but went back to my original Communing spirit spammer (once I got Ritual Lord), and never went back, never bought any more skills. I've captured a few skills here and there, and tried some weird builds (like an ashes trapper, and a pet/spirit build), which were fun, but there are so many skills I haven't bought and see no need to buy.
On the other hand, my Necro from Tyria has almost every Prophecies skill, and loads of elites, a handful of Factions skills and a couple elites. I have used almost every skill in one build or another. This could be a flaw in the design of the Ritualist vs. the Necro, possibly, but I think a lot also has to do with 'raising my character' through the different campaigns.
I dunno, this is all my opinion, of course. Just the way I see it.