ElRay: Trying a number of variations, I found that setting the "perpendicular" fret so that the nut and last fret have equal angles works the best for me (Some folks also consider this more aesthetically pleasing). Doing this, will, more likely than not, leave no frets perpendicular. IIRC, depending on the number of frets, that point will likely be between the 7th & 8th or 8th & 9th frets. FretFind 2d makes it really easy to tweak the "perpendicular fret", so it's not tough to match the nut and last fret angles.
I think either method will give you a range, as it's impossible to tell exactly what the angles of the bridge and nut are, especially at a distance, due to perspective.
bostjan: Not having the 12th fret perpendicular does result in the bridge being at a sharper angle, so depending on your choice of bridge, you may have to go with the 12th (or higher) fret being the perpendicular fret.
I think the aesthetics are an issue for many players, but I also believe that the ergonomics are equally important. It feels better to have the bridge at a more extreme angle, because there are no frets near the bridge. I find that the eighth or ninth fret being perpendicular feels most natural. Normalizing the fifth or seventh fret would give more leeway for having a tamer angle at the nut.
I've been thinking a lot about how aggressive a fan will suit me. Frets fanning out at the lower end of the board seems to be even be advantage, as it allows more space for firnger work. On normal axes, I often find the tightly spaced fretting limiting when going down on lower strings.
Towards the neck I'm more in doubt. What about barres? Not having access to fanned fret instruments, it still seems I'll have to angle my wrist out of proportions, or angle the axe 'up' for such grips. Am I imagining things?
If not, I think I'll prefer a not too fanned out layout (thanks for the FretFind 2D link, BTW). It may also work better with the upcoming Kahler's for fanned fretting.
Another issue is weight, sustain and tone. I've tried to poke info on cavity designs for some time. Lots of opinions, but I find it hard locating real knowledge about exactly which impact a cavity design has on tone and sustain.
Correctly implemented it may boost midrange tone and sustain.
I'm not interested in a jazz guitar tone (no pun intended). I'm interested in a well balanced axe with excellent sustain across the board.
I sometimes miss a more crisp attack and bite, especially at the lower range. This seems to be where a fanned fret design should really help.
I'm also interested a sweet midrange, kinda like what some ESP/EMG's exibit. This is where I feel a cavity design may contribute.