+1 on protective mods first. Be aware that on both my S1000RRs (2011 and 2015), putting in the case savers, which requires replacing a few of the case bolts with the provided ones, resulted in my bike leaking oil (very slightly) through the cases. Like everything else on these bikes, the case covers and gaskets seem to be very susceptible to futzing with them.
Regarding rearsets, if you need better comfort than factory due to your size/shape, then go for them as they are adjustable. Also, grip. I use Attack Performance and boy, are they grippy. And sharp. However, you will also need boots with replaceable soles, or you will be having to buy new boots when your rearsets chew through the soles. So unless you really need grip, stay with factory.
Unless you are an electrical engineer, skip the tail tidy. A friend gave me a Yoshi tail tidy that looks beautiful but I KNOW I will screw something up if I try to do all the cutting and splicing required. So there it is.
I also changed the ugly-ass stock brake and clutch levers as soon as I could.
Wait before you toss the stock exhaust can; it gets louder and throatier with age. If you still don't like the sound, then change it. So many threads on which one to choose. You can justify the expense by the weight savings and tell yourself you did good.
I put in a Brembo front brake pump. I don't think I gained that much. Less fade on the track. Maybe. I should have first played around with brake fluids and pads before spending the dough and spending money to have someone bleed it at the ABS pump under the seat... big PITA.
I put in a bubble MRA windscreen. Noticed nothing. Maybe looks better? Not sure anymore.
Went down a tooth in the front sprocket. Well worth it for my shorter tracks/twisty roads.
Luggage: Wunderlich small tank bag and rear seat bag: Awesome.
Invested in a Bursig stand. Love that thing.
SO, if I had to do it all over again:
Musts: Protection and levers. Love my Bursig stand (though it's rusting bad). Love the luggage, especially that front small bag made for the RR.
Maybe: Slip on or full exhaust.
Everything else: Meh.