I need to be honest with you guys: the older I get, the less fondly I look back on Suikoden V. Don't get me wrong, I still think it's a good game, but a lot of it's flaws are beginning to stand out to me.
Skill System - Limiting, inflexible, terribly unbalanced, and not fun to tinker with.
Towns - Sterile and uninspired with generally poor layouts. In particular, what really ground my gears was how the inside of most buildings were only a little more than concrete boxes.
Menu System - Suikoden III's menu system was sublime, with a clean design aesthetic, great information layout and sub-contexts sliding in and out smoothly. Suikoden V's system, on the other hand, was primitive, slow to load, and unresponsive.
Series Fan Service - More than any other game in the series, Suikoden V just bangs you over the head with references to past titles. In a lot of ways, I think that Suikoden V lacks its own identity because of this, with a lot of its plot structure and highlights being pulled directly from other games (II in particular).
Signs of Things to Come - A lot of the character archetypes and how they all interact with each other feel a lot more juvenile than in any of the games before it. Looking at the game six years later, I think that I'm beginning to see the underpinnings of the more otaku-geared Suikoden Tierkreis. This doesn't surprise me seeing as both games shared a lot of staff such as Takahiro Sakiyama (director of V, lead planner of Tierkreis) and Kazuyoshi Tsugawa (writer on both).