I have to go with Crusade's ending for a few reasons...
1. The final shot of them riding off into the sunset was just so perfect for the franchise and for who Indy was. He was never portrayed as the marrying type, so ending the franchise with a wedding just never seemed right to me. He was, however, portrayed as an homage to classic film heroes, and the entire series had been built on homages to classic adventure films, and that's why literally riding off into the sunset worked perfectly... it was one final cliche/homage, done perfectly.
2. I understand people saying that they always wanted Indy to end up with Marion, but I don't think KOTCS set it up properly. The wedding just seems to pop up as fan-service, without really building their relationship before it.
3. The Indy/Mutt storyline doesn't get resolved in a way that's nearly as satisfying as the Indy/Henry Sr. storyline did. With Indy & Henry Sr, we see them gradually gaining a true respect for each other, and when Henry finally refers to Indy as "Indiana," it's a breakthrough moment in their relationship. Nothing like that happens between Indy and Mutt. So, as a finale, it's not satisfying, as there's no real sense of character resolution.
Of course, neither one is the finale now, so I'm really interested to see how Indy 5 ends things, as I have to assume that will be the final Indy movie with Ford.