1) I would love to see Detective Boy finding that Sleeping Kogoro is Conan and help him with that. I think it would be a interesting change in the anime and a opportunity to develop them. To clarify, i don't want them to know that Conan is Shinishi, i only want that they know that Conan solves the cases instaed of kogoro.
2) Normaly i love that all paring get close at the end of the series. I hare inconclusive ends... But not in this case, i can't stand Ran and Shinishi, i really hate the paring. So i would love to seen a open ending (talking about pairings ONLY)
3) Haibara and Shinishi, both mistakenly taking the antidote and traying to hide until the effect ends.
4) More case with Sera and Conan, and only them, or Conan and Haibara or Ayumi. But again, the two of them alone i want to see them interact a bit more.
But i really want the first. (And i pray for the second)
And this is not a spesific scene or something but i want more cases where the culprit is not the one with the best alibi (Or the only with alibi, that is normaly the case). There are a lot of those and more in the newers episodes.
And those are the ones that i remember that i want, and that it could happen (Because there are a lot of thing that i would love to see, but it can't happen)