I just stumbled upon this thread and I realise Ive got here a bit late but as I have a little bit of experience, thought Id throw in my two pennies worth...
Not surprisingly given our joint experience, I find myself agreeing whole heartedly with Sheldon about string gauge. The truth is absolutely that longer scale length IS the answer to clarity in this context but so are string gauge and construction (we have always had ours made for this reason) and the resonant frequencies of the materials from which the bass is built. And its not just about low notes; half the point of having a B string is the access it gives you to patterns of notes higher up the neck and this is where the overall evenness of the string not only to its self, but also in relation to the rest of the strings, really sorts out the sheep from the goats!
Added to which, given the fundamental frequency of a B string is somewhere around 30 Hz; most back line amplification (speakers) cant come close to reproducing frequencies that low! So most of what you are hearing is the harmonic content of the note anyway - so a lighter, more flexible string can only help...
The other, less definable ingredient is the materials from which the bass is constructed. Tone of a stringed instrument is about the transmission and absorption of specific frequencies and the more to the edges of the range we move the more critical this balance becomes... So, given the relative unpredictability that comes as part of the package when working with the also wonderful properties of wood, even with a lifetime of experience (I've been doing this since 1968 and started building extended scale/low tuning instruments nearly 30 years ago), there is always going to be an element of luck!
Electronics and pickups are important but only as a conduit for the natural sound of the instrument they cant transmit what isnt there!
So, in short; the answer is undoubtedly a longer scale length, a lighter string and a well constructed instrument built from a balanced selection of materials...
Good Luck!
Chris May (Overwater Basses)
Sorry to dig this up after it lay dormant for a while, but I wanted to chime in, since I've always got an opinion.
I agree with Chris on this.
From my experiences, I've come across basses that were built specifically as an experiment, such as the famouns Stambaugh twins where the only difference between them was that one was 34" and the other was 35". There was a difference between the B strings on these basses - in fact there was a difference between all the strings on these basses. The 34" Stambaugh had a good B string whereas the 35" was a little more focused.
The thing is, if you're in the camp where adding the extra inch and ignore everything else, you're doing yourself a disservice. Between the two basses, I actually found the 34" had a "good enough" B string and was more comfortable to play. It also sounded less "twangy" on the G string.
There have been a large number of posts regarding scale length, continually since the dawn of TB! There does seem to be some consensus that scale length is but one factor, but certainly far from the single answer. Other things many have come to agree with is that the stability of the neck and neck joint are factors as well.
To add on to Chris' comments above, I noticed (supported by his actual comments which are available somewhere) that Mike Tobias has commented on the harmonic content, as well. When you look at construction of the neck joint, bolt-on necks have a perceived increase in harmonic content, which makes bolt-ons seem more focused. OTOH, neck-through basses have an increased amount of perceived fundamental content, which can make the B string sound more full.
Some luthiers have mastered their construction methods to consistently produce basses with great B strings regardless of scale length. Jerzy Drozd and Sadowsky are perfect examples! I own a 6-string Jerzy Mastery with a 34" scale that has a tremendous low B. I've never played a 5-string Sadowsky with a 35" scale, but all of those that had 34" were equally tremendous. Other highly respected luthiers produce 35" scale ERBs almost exclusively, and also with great results, such as Roscoe, MTD, and so on.
What's your preference? Mine is to find a good low B in a 34" due to playability.