IMHO, what made Suikoden different from other RPGs are these:
1. In many RPGs I have played, experience points given by enemies are fixed, but the experience points required to level up a character increases as the level increases. This will give rise to ridiculously repetitive grinding, since EXP from monsters grows linearly, whereas required EXP to next level grows exponentially. For example, at Level 1, enemies give you 5 EXP, and you will need only 10 EXP to level up. The next 5 levels or so, enemies give 10 EXP, but you will need 100 EXP to level up. Isn't that great? You're going to waste time grinding because you don't want the boss to mop the floor for you. Result: You lose focus on the real story of the game.
2. Damage dealt to and received from enemies is a function of a character's stats and of a necessary modifier that is usually a power of 2 such as 16, 32, 64, etc. Formulas for damage are not as straightforward as the average player would understand. The same thing with stats, too.
3. Mages and/or any characters that can cast spells are overpowered in many RPGs because they can spam offensive and supportive spells like there's no tomorrow, once they reach a high enough level. You ran out of MP? Just chug bottles of blues, if you know what I mean. Thus, physical characters are often overshadowed late game and only become the heavy duty tanks of the party. Reason? Pure swordsmen here suck endgame. Period.
1. The EXP system here is unique because while the experience needed to level up is just 1000 points all throughout the game, EXP received from mobs is a function of the difference between the character's level and the enemy's level.
That way, you will become strong enough to beat the boss by the time you fight him,(READ: WITHOUT EXTRA GRINDING). It doesn't matter if you entered the final dungeon at Level 1. You will still end up strong enough to defeat the final boss with ENOUGH grinding. Other RPGs practically don't allow low-leveled characters to high-level dungeons, and all characters are within the same level range as each other.
On a side note: The only reason you will grind in Suikoden is because you're farming runes, weapon sharpening fees, and equipment for a desired party.
2. Managing 60 or so characters, six persons at a time, sure isn't a walk in the park, but is definitely more fulfilling than micromanaging only like three or four characters at one time. You get to choose the party you want, or you can bring in the "iWin" party. It depends on the player, so you don't have to get stuck with 4 overpowered characters all throughout the game, as if you are left with no choice but to use them over and over.
3. RUNES. A unique spell system wherein powerful skills are balanced by allowing the player to use it a limited number of times (the only way you can restore your spell charges is by resting in an inn. no blues required, no spamming O_O), so that you won't have to rely too much on just rune spells when your front-liners can protect your casters at the back row and can dish out good damage to mobs as well. And runes are not just limited to magic. Some of them can be used to improve the character's innate (as well as the not-so-innate) capabilities.
But the most compelling reason why I prefer the Suikodens: their stories. They're not just some fantasy stoies about young warriors battling against evil forces surrounding the whole world. Their stories are based from real-life wars, and often depict the more human side of politics and war. Just reading the Suikoden stories without playing them is a crash course to politics for me. It is true that wars compose of opposing forces. It is true that wars claim so many lives. But the fact that they believe in something, that somehow they can change their destiny and that they are willing to die for it, is outright idealistic.
It's not all about knowledge, but it helps.