I've had mine for a couple of years now. First thing to do is verify the maintenance items are tip-top. These include all the electrical connectors are clean and tight. Battery top notch. Alternator brushes proper length. Clutch spline lube (which leads to the clutch inspection, oil seals, swingarm bearings, paralever bearings), fluid change (no solid metal flakes on the magnetic plugs for the rear end or tranny), good carb cleaning (remvoing float bowls and jets, maybe replacing needle and needle jet due to wear).
Upgrades? Suspension and brakes. I have a Fox rear shock, and the Race Tech valve in the front (along with Works Performance springs). The Harrison caliper I have is nice, but do a steel braided line first, and then think about a caliper and/or rotor swap. I've also done some little things, like changed the charging circuit a little bit to minimize losses, added a voltmeter and ammeter to monitor the crappy system. Ricky bars! Need I say more. I removed the stock speedo and use a Trailtech unit. THis allows me to remove the speedo drive cable from the tranny (and another spot for water to enter). I relocated the negative cable to the right/lower tranny/engine mounting bolt (no broken rear tranny cover for me!). I raised the seat. I've installed oilhead pegs for better wet traction (though I still need to lower them to the stock USA GS height). My bike came with Touratech bags, but I'd probably buy Ortilib dry bags instead if I had to.
Christ, the list goes on. I'll think of more tomorrow.
"I don't know what you do, but I know what I do, and I don't do that." --Uncle Doug, R.I.P.
"Without the possibility of death, adventure is not possible"--Reinhold Messner