Not exactly a problem for Nintendo. Considering how few titles were sold, it's not hurting them to lose it, and it's not going to hurt Sega either. Gamecube was screwed from the beginning for multiplatform sports titles. They are competing with Xbox mainly, and Xbox will always have the better graphics and better sound out of all 3 versions. On top of that, since Nintendo chose not to release the SD cards, they are forced to cut some features, while Xbox features a HD and allows you to save numerous franchises, seasons, and anything else your heart desires. Now with online play, people will either choose PS2 because that's all they own, or go with Xbox. It's not a bad system for all sports games, but it gets killed when it comes to the big sim games. Can't blame Sega here.
Porting isn't a surprise, considering many of their titles didn't do so well. JSRF comes to mind. Why not try putting it on other consoles? You never know, might catch on with a different crowd. Shenmue won't, and you know it. It's always been a game meant to be played on one system, through the multiple games. It's also a game that thrived on having cutting-edge graphics. Combine that with Xbox having the fewest limitations, and you know Shenmue III will be Xbox-exclusive.
VF would make sense to port, but they need to get it done before they're over-run by MK
A, SC2, and DOA4.