In my opinion, there really are no "cons" in regards to adding Williams engines to a layout. I am assuming you are comparing postwar Lionel to Williams. If that is the case:
1. Williams uses can motors and an electronic e-unit. Quieter, smoother, and pulls more than postwar, but no "ozone" smell, and that special something that comes with an open-frame AC motor. A Lionel postwar 675 comes to mind here. Mine is like a Swiss watch, where my Williams berk. is a Timex.
2. Appearence: I have 2 Williams F-3 sets. Santa Fe and Rio Grande. They look great! The thing is, when comparing them to the original postwar units, they look different. It seems that to my eye, I am used to seeing 50 plus year old paint jobs. I have no doubt that Williams got the graphics and colors correct, I'm just not used to seeing "brand new" postwar F-3's!
3. Repairability: Both postwar Lionel and Williams can be repaired, just differently. The postwar engine consists of a relaxing afternoon removing the motor (s), cleaning the engine, replacing worn parts, lubing, and putting it all back together. I enjoy this type of work. The Williams, on the other hand, consists of replacing the can motor with a new one, or replacing the truck with a new one. That is if you don't utilize the lifetime warranty that comes with the engine, and just send it in for repairs. With Williams you replace what doesn't work, and with postwar Lionel you fix what doesn't work, kinda like new cars compared with old cars.
I won't say one is better than the other, just different. If you're used to postwar Lionel, the Williams will seem "odd", in regards to the above, and vise versa. If it was me, I would go ahead and buy a Williams engine and see how I like it.