Hmm . . . it's a little hard to compare the two vehicles, but I'll try.
The shifter was a lot smoother on the S2K, and it had to have had a much lighter flywheel. Noise-wise, hard to say as that entire car was noisy (which might be why the Z never bothered me). But I say that it's hard to compare because the S2K was so low on torque, and it had a 9000 rpm where you didn't even really get any decent power until 6000 rpm! So it's easy for the transmission to be smoother on the S2K when it didn't have to handle as much torque. Plus that flywheel had to be light in order to spool up to 6k rpm in a half-decent amount of time, and I think the lightness of the flywheel also aided the smooth 'feel' of the transmission. You know how in the Z if you downshift without rev-matching it feels really jerky? Well in the S2K you could downshift like that and the transmission would hardly jerk. It'd 'absorb' the mismatched revs much easier. That's all down to the weight of the flywheel. The reason it jerks so hard in the Z is because it has a heavy flywheel, which means more rotational inertia. So the S2K's tranny was smoother, but it's easy to be smooth when you're low on torque and have a lightweight flywheel. Swapping the Z's stock flywheel for a lightweight one would help, but noise will go up.