Could this work?

We've all had our autofill woes, but Riot insists it's a necessary evil, otherwise we'd have to deal with very long queue times, especially in higher brackets. What if autofill was optional but rewarded. The reward could be simple, such as, for example, bonus IP (or XP in the future). Someone who queued with autofill enabled could received a bonus 15% IP that increases to 30% if they're actually autofilled.

By balancing the incentive, Riot might be able to allow players who don't wish to be autofilled that option without increases game times.