I think both had their drawbacks. A few comments regarding PIV and CV3D:
1 Workbench is obviously faster with P96, verifiable by benchmarks
2 CGX specific things, like most RTG demos, are nicer (smoother, better framerate) with CGX, even on the PIV
3 CGX emulation in P96 is broken on the CV3D in Z2 mode (no problem with Z3)
4 The CGX MEMCLOCK tooltype does _nothing_ on the PIV

I would prefer to use cgx due to #2, but the rather horrible/sluggish WB experience means I generally don't. I spent many hours fiddling with the tooltypes and env-variables (kept thinking "I must be overlooking something!!") to no avail.
BTW while CGX 68k might be dead, CGX is well and alive in MorphOS. It still beats the s**t out of Picasso96, too.
I can't comment on MorphOS CGX, as the last time I used it was years ago on 1.4. At the time, I ran some graphics benchmarks between my lowly G3 Pegasos and (then totally sweet) overclocked Athlon XP-M rig with WinUAE/P96... MorphOS/CGX was surprisingly faster, and not just a little.