Suikoden III had by far the best character development. It managed to keep a good 50% or so of the cast interesting. Even II and V only really managed to build up the main characters. I didn't even mind the battle system of III that much either, as it added some difficulty to a series known for being piss easy. The only critical failure was recycling the same 4-5 areas over and over again. With a half-dozen more unique dungeons, it could have been the best of the series.
I know a lot of people liked V, but I actually though it was the worst (not counting IV as a real game of course). It had absolutely horrible pacing, and often felt like the game kept going on for no reason. It was also the easiest game to break, creating chacters capable of one-shotting entire groups of enemies. And even if they didn't, you had 5 other characters ready to nuke the poor bastards afterwards.
Though one thing I'll give the entire Suikoden series is that is does a great job on the villians. You genuinely feel kind of bad when you kill most of them, and the crazy ones are usually crazy awesome. Especially compared to the FF series, which usually has utterly forgettable villians. Many of them in post-SNES FF games don't even have any sort of build-up, they just kind of show up, you beat them, and the credits roll.