Well, there are several reasons actually. The main is obviously for dramatic build up. If Muffy had appeared so early on in the movie and told Simba everything, there wouldn't be much of a story now, would there be?

Nextly, much like Kivuli stated, it's Muffy's spirit that's speaking to Simba and there's certain unspoken rules that seem to go with such things. The most important of those rules being that one cannot have a life altering vision until they themselves are ready to accept it. Nala appearing after being gone so long and her trying to convince Simba to go back, along with Rafiki's lecture were the perfect gateway to Muffy's appearance. Many argue that it was just Simba imagining his father anyways, and so his memory of his father wouldn't be able to tell him more than what he already knew of him, there for, the spirit couldn't tell him what exactly had happened, only that Simba was the rightful king, which was true and something Simba already knew but just didn't want to face.

For me, it was the perfect time for Muffy to show up in the clouds. Besides, there's not much Cubby Simba could have done about it even if he knew the truth right off the bat. Scar was just too convincing. Teen Simba was too busy slurping down grubs and snails to probably even care, so the only other option is Adult Simba.

This also gives plenty of time for character development and change too. You can't learn a life lesson in less than a lifetime anyways.
