Where this becomes a problem is if you get upgraded on a short connector flight followed by a longer flight.

For example, flying YVR->YYC->FRA. In the old days, I would decline the upgrade on the YVR->YYC portion if my YYC->FRA upgrade hadn't cleared. No way was I going to waste an SSWU on a 1 hour flight. In the new system, this becomes more difficult, though in my case I don't even bother putting in for an upgrade YVR-YYC

In reality this should be a moot point on many routes. If you decline your upgrade, there will often be someone else waiting for an upgrade. In effect, you're just trading seats.