True bypassing a Crybaby is well worth it in my opinion- some cats, however, do like what a stock Crybaby does to the signal, though (Bonamassa, maybe, IIRC).
It's all so subjective, but I TB'ed mine, intstalled an Area 51 buffer so it would play well with my fuzzes, and also did the "vocal" mod (changed the 33k to 51k) and the "mid-boost" mod (changed the 1.5k to 2.2k- I might actually pull this out and and try a 1.8k). I also lowered the input resistor from 68k to 47k (very important if you true-bypass it). So far I love it. Big improvement to my ears.
I true bypassed mine a few years ago. It does make a difference. I wouldn't suggest messing with the mods until you've done the bypass though. See how that goes first, don't try to do everything at once.