I think the reward for dungeons might be increased a little, but not as high as quests. Maybe 10 rupees less or something? As for retroactiveness, I think we should leave that, it's quite hard to fix that and work it in nicely, but maybe it's a good idea to give the bonus to people now in unfinished dungeon threads? That'd be a little easier to work into the RP and easier to change rewards if one would want to.
Increase a bit, don't make it retroactive. Most dungeons (IMO) just aren't as well-thought out/roleplayed as quests, since they have the natural limitation of being an actual place in the games, so their rupee reward should reflect this. Retroactive just seems a little lame, because people certainly weren't complaining before about the rupees offered by a dungeon.
I can't be bothered finding the topic but I complained in the past about the rupee limit, so the last statement is slightly invalid. :U