First, "harmoniously balanced whole while minimizing negatives" is what everyone should be aiming for - certainly what I'm trying to do. I don't think it's "fundamentally different" from most people. I love Nowitzki - I think most of us do. I love big men who don't foul (good ones are pretty rare). Jamison does have a significant negative, IMO - defense (more on that later).
Defense, you're selling short. It's absolutely not useless - if you don't have it, it can definitely hurt you. I don't think you can win a title without an 80+ big man and an 80+ guard - at least not very often. Take, for example, malone's team in the funk52 right now - he has a team with amazing rebounding numbers, incredible offensive efficiency, some of those great low-negatives guys you're talking about (Horace Grant, Kevin Love, Steve Nash not counting turnovers) but he's 36-32 and basically even in ppg - cause he just doesn't have much d. Solid team, not bad at all, but nowhere near championship caliber. In the playoffs, in these draft leagues, the teams are often very similar. Every little edge counts, and if you can't play D and the other team can, you better be significantly better offensively to make up for it.
Anyway, I think theoretically you could win a championship without a good defensive team - you'd just have to build an excellent offensive squad, one that can have a significant edge on every opponent to make up for the defensive difference. But I won this league last year starting 5 guys 80+ D, and only a couple low-minute backups under 50. I have no data to back it up, but somewhere in the area of under 50 or under 40 is where a guy can really get torched, IMO. So I try to have 80+ defenders that, between them, can cover all 5 positions (2-3 guys) and most or all of the rest of the squad 50+.
Also, I'm probably in the minority, but I don't even look at 3pt% at all. I agree we usually have great shooters as a whole, but you don't need guys who shoot 40+% from three. Lebron's 35% and below 3pt% is still very helpful. Mookie Blaylock is 43% from 2, 36% from three - but his efg% is excellent for a league at this salary. It's all about efg% (at least compared to fg% and 3fg% - ts% is a different story). I would rather have a guy who shoots 43%/36% than a guy who shoots 50%/40% if the first guy shoots a much higher% of threes and therefore has a higher efg%.
So, in sum, I think you have a perfectly fine system for team-building, I just think you're being a little too dismissive of some of the other approaches