I found Zool 2 AGA very jerky too and this was on '020. Certainly not the Sonic-style experience I remember from the ECS version of Zool 1.
Maybe it was designed on an A4000T... doesn't that have the full 68020 instead of the 68EC020 in the A1200 desktop?
I eventually sold mine and got the Atari Jaguar version of Zool 2 (which uses a 68000) and is extremely smooth, colourful and you can at last play tunes AND sound-fx at the same time. Syndicate is still better on Amiga than Jaguar though.
:-)
Smoothest scrolling platformer I've ever seen on Amiga is Kid Chaos - a worthy rival to Sonic games.