I was a huge fan of Rebellion back in the day and I also play EaW quite a bit still now. Essentially, EaW is a remake of Rebellion with a lot of added features like better graphics, ground battles, improved space battles, etc. but they removed a lot of very cool features that Rebellion had, like bombardments, planetary siding based on player actions (like blowing up a planet with the Death Star would often result in planets hating the Empire and siding with the Rebellion), and more special characters like:
- Bevel Lemelisk (superweapon designer who creates the Death Stars among other things, not mentioned until expansion)
- Crix Madine (Imperial Officer who defected to the Alliance, also appears in Return of the Jedi and Dark Forces and several novels)
- Moff Tiaan Jerjerrod (from The Empire Strikes Back, Return of the Jedi, and numerous Star Wars novels, oversaw constuction of Death Star II)
- Admiral Kendal Ozzel (executed by Darth Vader in The Empire Strikes Back, replaced by then Captain Firmus Piett)
- Commander Wedge Antilles (only X-Wing pilot to survive the attacks on both Death Stars, appears in EaW expansion though)
- Yoda (don't know why they left him out of the first game, added to expansion)
- Lando Calrissian (again, needs no explanation, but was oddly left out of EaW and the expansion)
The list goes on, but in all there were about 30 characters from the Star Wars universe for each side in Rebellion, compared to EaW's 7 Imperial characters and 11 Alliance characters. A lot of the characters in Rebellion appear in the expansion EaW: Forces of Corruption, but still not nearly as many as Rebellion had.
In addition to that, there are fewer choices for ships. In Rebellion, there were 19 different Imperial ships and fighters and 19 Alliance ships and fighters. EaW only had 14 Imperial ships and 13 Alliance ships (including special ships like the Millennium Falcon and Slave I).
Also, the Rebellion in-game Star Wars encyclopedia of everything involved in the game was a nice touch they left out of EaW.