II > I > V >> III >>>> IV
I could probably write a novel on the series as I've played each game at least 3 times and played I/II a total of 10+ times.
If II had V's war system it would be near GOAT level status. IV, to me, lacks any of the depth of the other games, you don't get that same attachment to Lazlo that you get to Tir or Riou. And his "hardships" are very meh compared to Tir and Prince. The war system in IV hurts it for me too. I like the idea of the navy but it still didn't seem to git into the series. I wish the storyline was better and the end game was WTF just happened? Not to mention 108 recruits, 4 man party.
If the first 8 hours of V wasn't so boring it would be at the top of the series but it takes forever to get going and then once it does get going you have some luck in recruiting some of the characters and then it takes time before the war system really becoems awesome. The War system in V is really epic, and I love the duel system as well. The formations were a cool addition as well.
Sui I maybe nostalgia but really it has the best protagonist, best rune, and it's story line is really epic. It hurts that its so short. And the rock-paper-scissors of the War battles/ only 2(3) duels.
II did everything gameplay better than I but I think the storyline took a bit of a hit and it kind of focuses on bringing back characters despite not really telling you why they are in the city-states, lol(why is Stallion running around there?)
III does have my two favorite characters of the suikoden series though. Futch is a badass and the GOAT enemy. I hated the paired parties though. And the game kind of goes into a lull after you finish the 3rd chapters until the final dungeon. Though Hugo's storyline is awesome, Geddoe is a sicko, and Chris is kind of a bitch. The War battles as extremely poorly done. Plus, outside of Hugo's early game, I don't really feel the plight of the main characters like the other games. I think that is where the first game really shines in showing the struggle of Tir(and its shown again in the second one).