A really cool plot might be that the Avengers time - travel to meet a young Stan Lee. They see how his early experiences and creativity are the seeds for their own existence in the Marvel Universe. He could inspire them in ways they didn't expect, like teaching them about the power of hope and imagination which then becomes a weapon against an enemy that feeds on fear. This would not only be a great homage to Stan Lee but also add a new dimension to the Avengers' story.
One plot idea could be that the Avengers find Stan Lee's old unpublished comic scripts during an adventure. They then use the ideas in the scripts to defeat a new, powerful villain who is immune to their usual tactics. Another could be that Stan Lee, as a spirit, visits the Avengers to give them moral support and some secret wisdom before a big battle.
Well, perhaps in the fanfiction, Stan Lee is actually a super - powered being in disguise. The Avengers meet him thinking he's just an ordinary man, but then they discover his true identity. He has the power to manipulate the very fabric of the Marvel Universe, and he enlists the Avengers' help to fix a tear in the multiverse that he accidentally caused while creating new storylines. It would be a really fun and unique take on the relationship between the Avengers and Stan Lee.