One more time because I just want to make sure it gets noticed (not sure how many developers were actually looking the Alpha Release 3 forums when this originally came out (it being a few weeks prior to Beta release and all that)).
The Fighter references the 3.0 Ranger
The 3.0 Ranger had the Favored Enemy class feature laid out like so: Whatever your first Favored Enemy is, the bonus against that creature type goes up by 1 at your next Favored Enemy selection, even if you now realize (or the campaign has changed to the extent) that your second Favored Enemy should’ve been the one picked first. They changed it in 3.5 to where you could pick which Favored Enemy got the additional bonus.
The Pathfinder Fighter, IMO, is making the same mistake. “Well, I started my Fighter thinking we’d be facing the same skeletons that the campaign started with, so my first Weapon Training was with Hammers. Now, I’m stuck with (eventually) +5 to all my Hammer weapons when I’d rather be swinging blades” (since the campaign has moved away from smash-vulnerable creatures).
I’d say make his additional bonuses function the same way as the Ranger’s additional Favored Enemy bonuses.