I've been playing through the series again and dispatched the first two incarnations with ease. Previously I would use a lot of powerful magic characters to do so, but this run through I decided on physical characters for the first two. The Beast Rune was still pretty simple with Riou's healing spells, Double-Strike and Friendship stuck on him. Unreal damage.
Suikoden III was a different story... I had only played through this once before many moons ago so the battle system still felt new to me. I actually struggled early on in the Geddoe chapters which was frustrating. The self-damaging Fire Rune and the Rune Skill System also aided to this. Anyway, the Wind Rincar took me at least 7 turns and 3 party changes to defeat. The Water Rune and Earth was by far the most frustrating part of it. When I finally got my breakthrough though Hugo and Fubar done the damage on it and finally... Success!
Suikoden IV I am now playing through and if memory serves me correctly I remember the Giant Tree being a total pain in the gluteus. Far off that fight the now so I'll reserve judgement for now.
Suikoden V I cannot even remember this boss fight... I'm gonna say it was reasonable thanks to the return of the six party system. I'll get back to you in a couple of months.