Yeah, there's quite a number of differences that make it worthwhile.
First of all, the Shadow Pokemon you snag can get unique moves they wouldn't normally learn in other games. Most of the time the move is either Refresh, Heal Bell or Helping Hand, but some of them can be very useful, such as Zapdos who gets among other unique moves Metal Sound.
Second of all, the game is longer and much more substantial than Colosseum. You'll be starting off from L10 rather than L25, and the opponents go just as high, so it's more of a challenge.
Third, once you complete the game, you can get a Lucky Egg without having to spend months hunting down Chansey in FRLG Safari Zone. (Note: you can also snag a Chansey if you have trouble getting those). Lucky Egg is a held item which increases Exp gained by 1.5 times, making level training much quicker (and it stacks with traded Exp bonus as well).
Fourth: you can choose which Eevee evolution you play with throughout the game. Not that Espeon and Umbreon aren't very cool, but each has their own merits. Unfortunately you only get one, and can't trade off for breeding until after completing the game.
Fifth: You can get Lugia, one of the few legal ways of doing so. The other is via the Mystic Ticket, and they are only usually available at one-off special Nintendo events.
Sixth: You can get all three of the Johto starters, each sporting their respective Elemental Hyper Beam moves (Blast Burn for Cyndaquil, Frenzy Plant for Chikorita, Hydro Cannon for Totodile).
Just a few reasons to get XD.