I posted to reddit/askscience/. I posted to Quora.
Then I realized there is a website where someone might actually KNOW whats going on!
So I present to you the best explanation I've found so far from wikipedia:
Current methods can directly sequence only relatively short (300–1000 nucleotides long) DNA fragments in a single reaction. The main obstacle to sequencing DNA fragments above this size limit is insufficient power of separation for resolving large DNA fragments that differ in length by only one nucleotide. In all cases the use of a primer with a free 3' end is essential.
I'm interpreting the "insufficient power to resolve large DNA fragments that differ in length by only one nucleotide." to mean that as inputs you need lengths of DNA exactly ... 523 bps in length ( or whatever the machine specifies )
To ME ( with my limited knowledge of the subject matter ) this seems trivial. If what is needed is to "resolve" out DNA lengths with more precision why cant we just lower the viscosity of the gel, make the bath longer and run the electrophoresis for an extended period of time?
... but this still doesn't make sense to me.
In the process of prepping a sample for DNA sequencing the researcher will run a electrophoresis and remove a specific chunk of DNA corresponding to a particular sequence length from the gel.
The question is: Why are we selecting particular lengths of DNA instead of just using the longest possible lengths we've got in the DNA solution? Note: As each sequencing technology is different feel free to specify which you are most familiar with ( I'm interested in all their limitations )