Your point on morality checks is a good one. To bad none of them mean anything in the way you can interact with others or influence your "destiny" or your party destiny at the time the choice is made, such as a bad choice while in a group will leak down to everyone, same goes for a good choice.

faction hits are just cheap, and that what most morality checks control if anything.

We won't see a truly deep morality system even attempted in an MMO for at least a few years unfortunately.
Combining the complexity of say, Fable's morality system and Warcraft's scope would be a truly daunting task, but if I had to say what the future of MMOs would be I would certainly suggest it to be in that direction.

Certainly something to look forward to though.

I just did that "Prisoner quest" in TR with its "moral choice". The prisoner is an insect-like alien that is a member of the race that just took the Earth from us and is trying to exterminate the last of our race. There isn't much of a dilema IMHO.
When I did it, I was thinking "yeah do whatever to it, gimme the chaingun".
There were a few other quest like that in TR but overall they didn't have any real impact on anything.

Again I will fall back on what I said before. This is WoW we are talking about. There is nothing in this game that goes to the sort of depth he is talking about. WoW is about harvesting points and getting uber loot. That's it.
Bartle needs to stop playing so much WoW, he reads into way to much. :) Didn't he write an article about how he would shut WoW down because he thought it was a horrible game? Why's he playing it?

Play EVE! Lots of moral choice in that game and you don't need an NPC to hold your hand, you gotta figure it out on your own.

I would love to read some of his "observations" after playing a month in EVE.

Thing is - with all this new "phasing" stuff they're doing, WoW is in the perfect place to do what TR didn't/couldn't, by offering you choices in how you complete quests that DO have long-reaching effects on the game-world. Players who make different choices could end up in different phases. Choose not to torture the prisoner? Fine - he becomes the lead-off to a quest chain that gets you entrance to a secret sect in Dalaran. Do torture him? A town that would have been razed is saved and becomes a questing hub.

The closest thing WoW had to that was the way they implemented choosing between Aldor/Scryer in TBC, and that only really affected your faction standings (which implicitly changed the landscape by making some NPCs hostile to you) and who would offer you quests.