It's just that (to me) the Mk2 with CVT was perfect. The Mk3 isn't. The implementation has its flaws and it doesn't seem to have received the same level of thought that went into the Mk2.
IMHO the nub of the issue is that the Mk 3 has a dual cycle Atkinson engine for economy. This means the CVT has a more complicated job to do than the Mk 2. In trying to respond to the driver demands it also has to consider which cycle is in operation and what will happen when when the cycle changes etc. It is another factor.
The net result is occasional slightly less automatic response to the accelerator while it ponders these issues. The power and acceleration are there, but not as readily.
The payback is the better economy of course.
As the previous owner of a Mk2 and Mk1 (still have), the answer to your question is that the Mk3 is definitely a better car than the Mk2. I would particularly mention the steering, which was awful on the Mk1, better on the Mk2 and right on the Mk3. Also rear seat leg room.