The integration of TFG into TCG league is most likely planned during the conceptualization of the TFG.
I believe whoever designed TFG in Japan even has plans to integrate TCG (or TCG-like) elements into the TFG game-play in the future (or vise versa).
This is pure speculation, but my reasons revolve around the three unexplained gameplay elements on the TFG figures.
1. There is no explanation for the Pokemon Type symbol displayed next to the Movement Point on each figure. These symbols do not appear anywhere else in the Pokemon franchise other than in the TCG game; the animation and VG both utilize the 17 type system (I realize the 17 types can be mapped into the 9 types). To reuse the same symbols on the TFG figures is an indication that the designers want to keep the TCG and TFG closely related.
2. Underneath each evolved pokemon figure has the name of the pre-evolved pokemon printed. Based on the current TFG rule set, this information does not provide any value to the game-play. However, this can to be an indicator that future rule set may allow basic pokemon to evolve in a similar fashion as the rule set for the TCG.
3. Each rare trainer figure has a blue semi-circle on their dial that doesn't serve any purpose right now. The WoW TCG popularized the avatar system with their HERO cards. MTG followed suit by introducing the Planeswalker cards two expansions ago. Maybe Pokemon TCG will use the trainer figures from the TFG set to introduce some kind of avatar system in the future.
I am glad Pokemon USA is putting more effort into support the TFG, which had a really poor marketing plan as far as I am concerned. There was one IGN interview that wasn't promoted on the official site. Penny Arcade did one panel for the TFG, and I am not sure if that's arranged viral marketing or just free prop because Gab and his partner think it's cool. Was there even a TV spot?
I also hope Pokemon USA fix the totally screwed-up packaging design by the release of Groundbreakers. The current packaging is prone to in-store tempering (secret figure theft is common in chain stores), not very protective (OH-HO death chamber), has large gaps in the starter backboard seal (the mat/manual packet can fall through the gap), and weird figure distribution (hooray for my 15th Zangoose in the secret figure slot).
