Here are the only inherit difference between the two of them. The size of the group. That is it.
The way the reward loot is slightly different and is most likely going to stay that way, but Blizzard could use either model for either size. Right now normal and LFR use different methods of loot, but they didn't always. In this case scenarios are the LFR, as they use a method of loot much the same, but they could switch scenario loot to be the same as five man loot having X number of bosses that loot tables.
Justice and valor points. Blizzard can set up a system where either rewards more a less for each done. They could make one reward 10 and the other reward 100, that is just a place holder.
Speed. Do people really forget Azjol-Nerub,Trial of the Champion, Forge of Souls, the old scarlet monastery... scenarios right now are faster than five mans, and a whole they are as well but there have been five mans that are as fast if not faster than the scenarios we have now.
Story. Scenarios do not inherently bring anything to the board that five players do not bring. They have chosen to design scenarios in such away that many of them have a more story based interaction that most five players, but I dare anyone to tell me that it is impossible for them to balance scenarios for groups of 5 over groups of 3.
PS. This post is about 3 player scenarios, and not solo scenarios.