Pokémon Emerald version is the special edition of Ruby and Sapphire, much like what Yellow was to Red and Blue, and Crystal was to Gold and Silver. Being a special edition version, it brings plenty of new features to the games. So what's new you ask? Read on.
The biggest change is the revised Team Aqua/Magma plot. While in the originals, one of these teams was trying to awaken a legenday Pokémon in order to fulfill their evil plans. In Emerald, both teams are evil and both have to be stopped. This leads to more logical fights against them, for example, Aqua is battled at the ocean reasearch center, and Magma is battled at Mt. Chimney. In the end, the only way to stop them both will be by awakening Emerald's box legendary, Rayquaza. Unfortunatly, Rayquaza can't be caught at a low level, and you still need beat the Elite Four before you can catch it.
There is good news though. Both Kyogre and Groudon can be found after beating the Elite Four as well. A quick visit to the Weather Station will reveal their location to you, but if you take too long to find them, they'll move. Groudon will be found in a cave and Kyogre in an underwater spot. Other changes to the legendaries include the ability to chose whether you want Latios or Latias, and a change to the Regi puzzle.
Another plot change is that Wallace is now the Pokémon Leauge Champion. His gym is now run by a new character named Juan, and Steven Stone can be battled as a super-powerful trainer in the depths of Metor Falls, a nice allusion to the battle against Red in Gold, Silver and Crystal.
In Emerald, all contests have moved to Lilycove, and the other contests have been replaced with battle tents, places where you can battle according to special rules. After beating the Elite Four, you will be invited to go to the Battle Frontier, where you'll be able to battle in several facilities that offer alternate rules much like those at the battle tents. An example of these alternate rules is the Battle Palace, where Pokémon fight on their own instead of taking orders from their trainers. The Pokémon will choose their moves based on their nature so be careful what moves you teach them.
Some other things that have been added are minor, but nice. A couple examples of this are the return of sprite animations from Crystal and the addition of a warning when the PP of a move is running low by changing that move's color, a feature that was present in FireRed and LeafGreen, but not Ruby and Sapphire.
All in all, Emerald is a decent game, but not enough of an upgrade over Ruby and Sapphire to get if you already have one of those games. If you have never experienced Hoenn before, then by all means, Emereald is the game to get. It's more complete than the other games and offers more to do post-Elite Four. Of course, if it's not a Hoenn adventure you're looking for specifically, you're better off with one of the newer games, which offer even more than Emerald.