Emerald was the "Director's Cut" version of Generation 3 just as Platinum was the "Director's Cut" version of Gen 4. What that means: Its the same story, fused with the Director's personal additions. Its the story that the Director wanted to produce. If you watch movies that have Director's Cuts there are small differences, usually different endings or parts changed/removed/added. If you haven't, go watch Salt. That has three endings that effect the the way the story goes through all the way to the ending.
These were special stories that the Director, Junichi Masuda, changed from the main story. That's pretty much all that they are. Which counts for Platinum as well. They are the only two Director's cuts that I know of as Yellow was a special Anime addition, Blue was the same as Red and Green, and Crystal was a completely different story focus Legend wise.
So there isn't anything that's heavily different other than all the extra coding they added to the stories, such as specific team meetings and Magma's new hideout, which can transfer over.