1. The world. The world is one of the most engrossing and genuinely fun RPG worlds to date. It's incredibly huge, incredibly detailed, and filled with tiny, yet colorful details (in the form of discoveries) that add new chapters of history and interest. The sense of discovery is not only a vital part of the world map on a whole (which combines the only really fun part of an overworld system, and that is airship travel), but also a central theme to the plot as well. The locations themselves, while cliche, are presented in a vibrant, lively, and genuinely swashbuckling. It's really hard to NOT like the areas, considering the amount of effort that's placed into making them not only believable, but also fun to spend time in.
2. The soundtrack. The soundtrack is really really great--again, along with the locations, each of the songs not only fit the locations, they also add an extra poignancy to the dramatic scenes. Sure, there's some crummy voice-over clips that happen during some dialogue scenes, but you can't really deny that the soundtrack fits the pirate and exploration theme to a tea.
3. Characters. Yeah, ok, some may give me some crap for this. In truth, I suppose, the characters are fairly cliche. In fact, it may be better to say that the "characters" part is better turned to the "dialogue" section, because the game's script is freaking FANTASTIC. There's no voice acting, but every character has incredible amounts of life and vigor. Gilder is possibly one of the most likable characters ever to be made, but every one of them has a spot in the limelight--even Fina, who is painfully close to being a total cliche ends up becoming a truly interesting character thanks to decent writing and plot development.
4. Airship Battles: They take the basic battle system and add a cinematic flair, some nifty tweaks, and an extra edge of difficulty and come up with something truly interesting. If you ask any Skies fan what their favorite battle was, they'll likely tell you it was one of the great airship duels, whether it's with an enemy ship or with one of the monstrous Gigases. Plus, you can recruit a wide range of colorful crewmates that add special abilities to your ship's roster, which adds a fun sort of Suikoden side-quest to the game's already huge number of cool things to do.
Plus, in addition, most of the slow-down and loading problems were solved in the Gamecube port. So, it makes it even MORE AWESOME.