Re: AlnicoII v. '59
i like the stock gibson 57s in my 335 - they are alnico II. BUt i also really like the sd 59 (alnico 5). I think with a twin and all that headroom then the alnico II in the neck will sound warmer, and maybe a 59 in the bridge for a bit more bite and kerrang (if that's a word).
Having said all that - if you are really into a warm jazzy tone, then use flatwound strings (thomastiks are the best). You may find the sound a bit of a shock at first, but once you get your ears around them you will be hooked. You might even find that you roll off even more treble with the tone knob after a while. Of course roundwounds are more versatile if you want to play other styles because of the extra harmonics in the note, but for a strong fundamental and a direct, subtle and responsive pure jazz tone then roundwounds are the only way to go. Of course, you have to play light and nimble to get the best out of them. There really is nowhere to hide if you go for this style. Digging in may sound great on a les paul with roundwounds into a marshall- same goes for a strat with some overdrive. Flatties require a light touch and subtlety.
Still, if you stay with roundwounds, then you can get a pretty sweet sound just by rolling the treble back to the point where it begins to darken. That is of course, after rolling the treble back on your amp to the same point. You will get a nice thick, warm sound. Play light with a heavy pick and you will get plenty of sustain and dynamics.
Re: lack of respect for pIIs. Most guitarists play rock/blues/metal. Some dabble in jazz, but very few devote themselves to the style. The A2 is for people who can hear the difference between one clean jazz tone and another. The subtleties are often overlooked by folks who prefer different styles. All of seymour's pickups are good. It just comes down to finding the one that suits your requirements. No pickup can do all styles and sounds.
So i guess all this means that swapping pickups makes a noticeable difference, but the real way to get a warm jazz tone is through a combination of other factors as well.