I miss:
"Center View on Now Time"
Screen Sets
Mix Recall
Copy/Paste Special
Nudge from one track to another (pressing 2 or 8 on numeric keypad in SONAR)
Being able to set separate points for loop and punch. In S1, loop and punch share same selection only...
Track Templates
Ripple Editing (Does S1 have this? I haven't found it yet...)
I am sure I will discover more as I get deeper into it.
However on a positive note, I like the integration S1 has with the Faderport. I also like the colors and themes.