I believe if the match were played in the early rounds up to QFs, Lin Dan would come out on top just as he did against the redoubtable LCW. I suspect after beating LCW with aggressive play, Lin Dan was 1/3rd if not half spent, and then Huang Yuxiang pushing him to three games in the SF stretched him thin to half spent force.
In the final, had Lin Dan taken G1 instead of losing it narrowly, 19-21, he might have a better chance of beating the top form and much improved Shi Yuqi, perhaps in two straight games even, who knows.
Nevertheless, take nothing away from Shi Yuqi who played excellent throughout the tournament, disposing of the likes of Lee Hyun Il, Chen Long, Son Wan Ho and Lin Dan, to crown himself All England Champion, a highly prestigious, top tier tournament that many top players are gunning for.