Jakandor was neat because it broke so many D&D conventions that it really became it's own game, a sort of sub-game of D&D. It was less D&D than even some of the strange settings like Dark Sun and Spelljammer, because at least those games still had wizards and clerics.
In Jakandor, you really had kits defining your class abilities so that, in effect, your kit was your class. And some of those kits were just neat. I remember the Charonti side (the Aztec casters) a lot more than the Knorr... the Charonti had kits like the Warden (a warrior that lacked the knorr's martial skill, but commanded a small crew of skeletons or zombies that he could boost with limited buffs), the Galvanist (a tinkerer that played with lightning, and actually attracted it if he got anywhere near it) and - my personal favourite - the porters (masters of teleportation, and the best scouts the Charonti had available).
Alignments in Jakandor didn't mean as much, since many Clerical alignment-based spells didn't exist, and the Knorr and Charonti were both equally "good" - the campaign wasn't built on the assumption that players would be on side X fighting against side Y, which was the tact used in pretty much every RPG up to that point. Instead, both sides had their own book, and the players could choose a side - and whether their goal was to destroy the opposing side, unite both sides, or ignore the conflict in search of your own goals, the game would work just as well.
It was also a game that didn't truly rely on magical items, though this isn't a big deal in 2e, where magical items weren't as built into the game as they are now.
It also lacked much in the way of healing. While clerics did exist, they were not as prevalent as they were in other games. When we ran it, we didn't see clerics at all, but instead used a primitive form of Reserve Points.
Monsters were generally better thought out, since most of the weird ones were either a result of the magical plague brought on by the ancient Charonti, or experiments gone awry. Also, the game lacked non-humans in any large numbers, meaning there were no elves, dwarves, halflings, or anything like that. There WERE crabmen, and a few other intelligent humanoids, but they were very minor players in the conflict.
Oh, and many D&D spells just didn't exist in the game. I've always said that if you take out the iconic spells like Fly, Fireball, and Magic Missile, the flavour of the game will be entirely different, and Jakandor is where I learned that. The spells here are just... different from what you're used to. And one of the goals of the Charonti is to rediscover the lost spells from the Charonti of old, which is, in my opinion, a great goal for PCs to work towards.