I think I'm one of the few who prefer IV over III.
The cons:
III has the "Trinity system," in which there are three main characters and the first half of the story is told three times through each one's perspective. And then a fourth character's. As a result, there's no central character that the people look to for leadership, or that you identify with(which is ok, except then it doesn't really feel like Suikoden anymore). Oh, and the castle never really transforms from a wreck to a your home(especially as you're kinda renting it from the fourth character). You also have to hoof your way around most of the continent.
IV suffered from a very large world that is only navigated by a very slow, awkward sailing process, and a main character whose polygon model looks retarded. (His character art is fine though)
The pros:
III has a kickass anime intro, and the characters are all reasonably cool.
IV castle-ship rocks, and Kika is hot. Also, its save-data loads in Tactics, which leads to some nice character development and conversations. Also, the slow-ass sailing is somewhat negated by the fast-forward button(R2), which can also be applied to regular field movement.