Suikoden 4 had a lot of problems. Not to say that is wasn't all bad, but even the good things had issues.
-improved trading system: trading had previously been nothing more than a convenient way to get some extra money. In 4, you have to rigorously trade in order to acquire the materials needed to make armor and clothing, which I personally felt was pretty cool. unfortunately, with various trading ports occasionally being made unavailable, and without viki, getting all your high quality goods takes a lot of time and annoyances.
-making armor & equipment: definitely a growing trend among RPG's, the ability to get some use out of random items from trading. cool way to get fancy equipment without paying. unfortunately there wasn't enough flexibility with this, and you couldn't make unique stuff.
-nice interface: not sure how to phrase this, but I like the way that the characters move on screen as well as being able to to first person mode, although it would be nice if there was more interaction between the character and the environment, along with bigger environments, and non-disappearing character models.
Bland and boring combat system: only 4 characters, lackluster rune use, and almost no difference between various characters. every sword user has the same pose, likewise with other weapons.
no skill system: suikoden 3 made the skill system a viable way to make distinct characters, something fairly important with 108 of them. suikoden 4 decided not to use it, making a bland combat system even more bland, and bland and forgettable characters even more bland and forgettable.
mediocre characters: 4 chefs? really...did we need 4 of them? that and far too many mini game characters, and other characters that just seem to be there. Until you play through tactics, you wont know why half the people on your boat are there. and even then you still might not know for every one. some characters like Kika are well designed, but most are forgettable and once you get them, you'll forget they're even there. some people have complained that some character's are ridiculous to recruit, but having played previous suikoden's, the recruitment for suikoden 4 isn't all the hard, it's just a lot faster because the game is so short, so you will miss things because you're expecting a slower pace.
pointless villains: Troy could have been cool. in fact he was really cool for the first part of the game. then he's whiny for the rest of the game, and then duels you at the end. graham cray, underdeveloped. the kooluk-a bunch of goons there to annoy you.
hurried plot: the plot seems to be going somewhere interesting for a little while, but once you get kicked out of obel, the plot goes fast forward through what should have been a much longer more convoluted plot.
definitely the worst suikoden, although a decent game.