The Folding Knife is definitely a great piece of work. It has similar cynicisms as Sixteen Ways, but isn't as funny. Solidly excellent, though.
My favourite Parker for a long time was the Scavenger trilogy, first book Shadow, because it was just so mind-bendy - like Parker does the Bourne Identity, but with a lot more flashback chicanery. I think my favourite now is Two of Swords but it is very opaque - Parker's style is in full force and I totally understand how Alex could have had trouble getting into it. It was originally serialised as novellas, and each has a different POV, sort of baton-passing the story along from person to person, which gives an amazing sense of the scope of the world and conflict, but can make it harder to follow (especially because Parker has a tendency to not use proper names, just use "she" and "he", intentionally causing confusion). I love it because of that scope, and because it feels like the first time he's had a central female character who was really developed, and because the emotional throughline was outstanding. But it is definitely NOT the snappy Sixteen-Ways version of Parker!
(I almost wonder if he came clean as being Tom Holt because he wanted to get funnier with his Parker work...)