In a keeper that only lets you keep two guys you want the one with the highest ceiling, even if you have to wait a year. Upton, no question for me. The only thing that can keep him from eventual # 1 overall status is health IMO. I traded for him in a keeper that lets us to keep one OF and I likely overpaid based on current values but Upton could win me that trade as early as this year.
Position scarcity can change significantly in a few seasons but health permitting Upton's status as a top three overall player could last 12 years or more as mentioned previously. If you think you're going to be in the league for a while, you want to be the guy with Upton. If he can build on last year, it's possible you might not even have to wait that long for the good stuff.