stout71 - I have occasionally pondered this issue as well. I always use effects, even if just a compressor.
One issue for you is fuzz. Generally, fuzz doesn't work well with active electronics, but it also works best at the front of the chain. One solution is the Z Vex
Mastotron. Another is to use a distortion pedal instead - there are a bunch of bass distortions available now that don't cut the low end (a potential problem if using guitar effects).
But then you have the issue of which pickups to put through which effects? A lot of it has to do with the type of effect. I could see putting something like phaser or echo on only the treble pickup. Distortion too - that's what Chris Squire of Yes would do. But now you don't really have to worry about losing low end with distortion - some pedals even have a blend control that allows you to blend in clean signal.
As I have posted elsewhere here, I have recently been using just the neck pickup, and at this point I think I personally prefer just going mono. If you are going in stereo, how are you summing the signals clean? Couldn't you just put the distortion on one pickup, leaving the other clean? If you want it on both, then why go stereo? Those are the kinds of questions that went through my head. You could use an F-2B or a mixer to combine the signals.
For fun, here is my board in its current state:
on/off (yellow box) --> MXR EQ --> CAJ V-Comp tube compressor --> MXR bass octave --> EHX Small Stone phaser --> Fulltone Bassdrive distortion
I intend to keep working on this - the EQ is to adjust for when I play with a pick - I am currently trying to analyze the frequency differences between finger and pick playing (look for a post in the future). I also need a (clean) boost pedal at the end of the signal for solos, which will probably take the place of the Small Stone. If I don't need the EQ for pick --> fingers, then it might end up being the boost so that I don't need to buy another pedal.
