Ahh, I see what you mean now. Essentially it is this:

--The only flights you can pre-upgrade to Stretch are flights sold as Midwest Airlines on midwestairlines.com

--Starting January 8th, all flights are only being sold as Frontier Airlines no matter which airline website you go to.

Therefore, at least at this point, for flights after 1/7/11 you can't upgrade to Stretch for coach fares until check in after 1/7/11.

Perhaps they will add this functionality to the Frontier site, or it may die with the Midwest site. But I completely see what you mean -- unless you're an elite level flyer or purchase a higher-tier fare from the Frontier site, you can't get Stretch prior to check in for travel arter 1/7/11.