Sounds like most of the problems people mention relate to things rattling. If you play the right kind of music, and your SW is up to it, things are going to rattle and shake wherever the SW is placed in the room! But, with patience, you can track each rattle down, and kill most of them.
As to height above the floor, I have just designed and built a SW system (3 of them to go with 3 front speakers) that is a bit out of the ordinary, but which I find very satisfactory.
My speakers are Magnepans, so I wanted a large radiating area of SW drivers, lightly driven, and I wanted them to sort of "play through" the screens. What I have (behind each MG1.6) is a vertical stack of a 12" Dayton Titanic SW driver and, on top, a 15" JBL LE15A LF driver. The center of this array is about 45 inches above the floor: nearly centered on the Magnepans. Crossover is 90Hz 24 dB. Accoustic foam covers the fronts of the SW enclosures except where the drivers are. (Good for the magnepan backwave).
I already had the JBL drivers, so the whole 3 set system, including lumber for the 7 cu ft enclosures buried in the wall, and three SW amps, cost less that what I was thinking of spending on a single Velodyne SW. Now the Velodyne is remarkable, but there is no getting away from the fact that it's only one 12" cone, driven very hard. I attribute the success of my design to the large cone area and the fact that it is off the floor.