Yeah, I've had both Geddoe and Hugo as my FCs (Geddoe as my favorite of the 3, Hugo due to being the "true" FC), and it does suck that with Geddoe, you basically lose out on the awesome True Lightning Rune. Although Geddoe is also the most competent with True Fire, so is probably the only FC where you could actually use it (in combination with Fire Rings and Fire Sealing runes). Hugo, of course, is the most easily justified from a story perspective, means Geddoe keeps True Lightning and Chris True Water, and I've found his chapters less boring in subsequent playthroughs than I did the first time. He also fits the basic mold of Suikoden heroes. But you'll never actually use True Fire with him, because it sucks and he's a great physical fighter.

The main reason I would ever choose Chris is to use her horse on the world map. Walking around in S3 was not my favorite activity.