Id like to share something they posted back in September regarding this issue...

http://forum.square-enix.com/ffxiv/t...on#post1251092

..where Camate posted they were planning to introduce a way to reallocate companion skill points. But.. its been seven months lol. Unless someone can find something more recent than the above.

So it seems the chocobo reset thing is very hard to implement (doubt it), there is some problem they foresee in implementing it, or is very low in their list of priorities/don't care right now (most likely). But either way id really like to hear any response from the devs regarding this.