Here's my list of pros for each:
Nolimits:
-Better Graphics
-Heartline display
-More options for stations
-Spinning coasters
-Lots of tools available
-Realtime numerical g-force readout
-Much better interface
-Camera tracking to trains in simulator
-Render to AVI
-Active development for NL2
Scream Machines:
-Single Interface for editing, rendering, and testing
-Autosave, which is good because it frequently crashes while rendering shadows
-Customizable trains, including multiple car types on a single train
-More coaster types, including 4d and suspended
-Custom ride music
-Dual loading stations and transfer tracks
-Up to 10 different coasters in the same park.
-Much larger workspace. I think the max height is only limited by the max number of track vertices.
-Detailed stats in editor to show time, speed, length, and forces for each segment
-Options to lock track vertices and handles to a specific axis
The frustrating GUI in Scream Machines was the main reason why I switched to Nolimits.
One specific gripe that I have with Scream Machines:
In Nolimits, you have the ability to select a track segment between two vertices. In Scream Machines, you just have to remember which way the train is traveling to know which segment is the one before the vertex you selected.