Based on your parameters, I would go for the 1999 model.
As the TJ got newer, they became more electronic and complex. That is why I also prefer the earlier models.
And you are correct that 1999 was the last year the TJ had a distributor. My 1998 model has 160K miles, and my distributor hasn't given me any problems. Just replace the plugs, wires, cap and rotor every 60K miles for basic maintenance.
In addition to a simpler ignition system, the 1999 model also has a much simpler exhaust system. The 1999 has only one catalytic converter, whereas the 2004 has two. And the 1999 will have only two O2 sensors, whereas the 2004 has four.
And if the 1999 model has an automatic transmission, it will have the very simple and archaic 3-speed 32rh. This is considered one of the very best automatic transmissions ever made by *anyone.* I think the last year for it was 2002, when it was replaced by a far more complicated (and problematic) electronic-controlled automatic overdrive.
And on a personal note, I prefer the interior and seats on the 1999 compared to the lowered seats of the 2003+ model.
Above all, I absolutely DESPISE that problematic multi-function light stalk that the 2000+ models all had.