I can understand why you have a problem with bone, ethereal and shadow... but i can assure you that spiritual damage is used in sooo many games. The fact that you consider this to be a "unrealistic" type of damage, leads me to the conclusion that you like to stick to the typical "warrior" style fighting which consists of mainly the bigger the sword the bigger the damage. A major factor in playing the role of mages and spirits is the use of spiritual damage.
I have hordes of 2E and 3E D&D sourcebooks, ranging from the core rulebooks to such esoteric, specific ones as
Unreachable East, Magic of Faerun, Dreams of Red Wizards, Book of Vile Darkness, etc. You don't get any more crazily detailed than this (psionics, clerical magic, the Weave, the Shadow Weave, druidic magic -- more varieties than you can shake a stick at. Shall I go on and detail the diversity of spells to you?). I have played Planescape: Torment, the Baldur's Gate games, Icewind Dale, etc. In all of those games, I've heavily employed magic-using characters, and trust me, both 2E and 3E are far more complicated than BD or DD will ever be. Except that there usually are reasons behind the complexities; there are backstories attached to various types of critters and species. If there are exlanations behind "bone" -- say, that necromantic rituals imbue the bones with special qualities that make it different from wood and metal -- I might accept it, but there are not. Ethereal, shadow and spiritual are utterly redundant; the three could have been grouped into one. For that matter, I think ethereal, shadow, spiritual and bone should have been grouped into one type, period.
I do think that they should have added more side quests... i like running around looking for the lost teddie style of quests.... especially if you need to go resque the cat that stole it, so that you can find out where he hid the treasure map, collect the half that the elf stole, and then fight through the dwarven dungeons to get to the cave, because the other entrance caved in, and on your way out a giant spider wont let you pass until you bring it the golden egg... You get the idea... i love those....
The side-quests in BD are cute and numerous, but the majority of them are just the generic "fetch this, kill that" fare. I prefer fewer quests, but with more depth to each. Take, for instance, Sunry's trial in KotOR, where you actually have to talk to a number of people and have multiple conclusions to draw, multiple solutions to choose from. Or PS:T, where intelligence/charisma/wisdom affects dialogue choices. See, the problem with BD, I think, is that there's too much of everything; resources are spread thin over them all, and none of them ends up with any real substance.
BUt yes i do agree that BD has its shorcommings... but i know that all these things will be ironed out in DD2. They tried something new, got the feedback, know about the good and bad points, so they can improve it and only have the good in DD2...
I am sorry that you did not enjoy the game, maybe you will love DD2....
I played DD and enjoyed it greatly for what it was -- a braincandy romp, traditional fantasy setting and all. Not much in ways of innovation or originality, but very fun, all the same. I think BD tried a leeeetle bit too hard, and I'll be much more wary when DD2 comes out.