I'm sure others will chime in with more detail but these are some of my own observations...
A2:
Pros - Nice compression in the attack, very smooth, nasally voice.
Cons - Can be overly bright, too compressed for some applications.
A5:
Pros - Open and airy, superlative clarity.
Cons - Lack of compression, can sound too boomy/chimey, lacks the musical character that gives some other magnets their unique voice, I find it more transparent which can be seen as a positive or a negative depending on the style of music you play.
Although I have to say that the short A5's I have in my new Throbak's are unlike any other A5's I've used before, they seem to combine the best qualities of A2 and A5.
Thanks RB, are those short A5's unoriented? Used in both neck and bridge?
...in my experience the Alnico 5's are more "modern tone." My suggestion is to go to the Gibson site and listen to the difference between any of their Alnico 2 pickup clips versus the Burstbucker Pro (which has the 5's).
It's funny, I've heard a few different things about the VLIII pickups and the magnets used. I think when I initially ordered them, he told me A4 bridge and A5 neck. Frankly, they are the first pickups that I've had which I have not even thought about swapping magnets. They are that good and more importantly clear. IF it is indeed an A2 in the neck, it will the first A2 pickup I have EVER actually liked, and in the neck no less. I'd be very surprised.