The friend's computer that I just worked on was built into a Nine Hundred and I ran into many of the same problems, but one thing I can say is:
It didn't have the side-panel fan, but all the others were installed and even at idle, a piece of paper could easily get caught on the side of the case where the side-mount fan should be. As far as mounting mobos go, I tighten the standoffs good, then tighten the mobo screws just enough to keep them in place unless it's a customer computer which will go into a home where I know or am relatively certain is void of computer literate people. Then I feel it's best to make it a little more difficult for them to do their own "work" on it and end up calling with a "I don't know, it just won't turn on...".
I have been eying the 690 II for a while now, but am still unsure of what I want other than the ability to upgrade to whatever behemoth graphics cards they brew up next.
EDIT: As a side note, there are two versions of the Nine Hundred that are of note, both of which have been described on this thread. I think one has the 1" screws and the newer one has the different mounting scheme. Since I don't own one, I cannot say for sure - I have a cheap(er) case with burrs and about 1/3 the airflow of an Antec Nine Hundred case.