and the M1000 has the same engine at the multistrimmer

- it has better power delivery than the S4, not as snatchy.
If you have the dosh, go for the multi as a commuter - as has already been said - its got more 'home comforts'.
If not got the dosh, then next my recco would be a 2nd hand or new M1000 (contrary to rumours, they have not been discontinued - just the 'S' model' ) then an S4.
However: on the roads I use for work, I wouldnt commute on my M1000 - I'd buy a M600/620 for that - so what I have said above would only relate if you didnt have a short/stop-start journey to work (I think

)
If wanting lower CC for cheaper insurance then maybe consider the M900 (ie models) - can pick up for about £2,500 - 4)
Also boils down to if you want an aircooled or if you like the plumbing on show.
I think you could have fun on the S2R - but it might 'pale' after a while - and it is also made as a 'budget' bike, so usual 4 pots are gone - replacement 2 pots instead, and various other parts cut back on.
My suggestion?
Keep the 996 for sunny summer - and buy a M??? for commuting on (if you have the dosh , that is!)
Happy shopping
C