I play by the rules in this case.
I think that the Fighter loses too much power if you allow feats to be banked. In general the fighter gains access to the most powerful feats one or two levels earlier than the barbarian, paladin or any other class. In some situations it can be 3 or 4 levels. When playing a campaign this has an impact on the relative effectiveness of the PCs. The other classes have their advantages, this is the fighter's.
For example, a Human Barbarian could take Power Attack and Cleave at first level, bank his third level feat and take Great Cleave at 4th level. So the fighter no longer has the option of having Great Cleave two levels before the Barbarian.
Example Two: Human Ranger fighting with two short swords can bank his 6th level feat and take Improved Critical (Shortsword) at Level 8 and Improved Two Weapon Fighting at Level 9. (If he can't bank those feats then he has a tough choice at Level 9, and has to delay taking IC for 4 levels or ITWF for 3 levels, relative to the fighter.) Now if he had banked his 3rd level feat to take Spring Attack at L4, then at Level 9 he has three "boss" feats instead of two. The distribution of the best feats is no longer weighted towards the fighter.
This is even worse if you are starting your campaign at level 6+. The PC's don't even have to put up with a few featless levels -- there is no disadvantage to banking feats in order to load up on the best ones.
Same deal for the Wizard, but the effect isn't as pronounced because they don't get as many bonus feats. Even so, a Wizard can take Craft Wand at 5th level and Craft Magic Arms and Armor at 6th level. Sorcerers, Clerics, etc. should have to wait until 6th and 9th to get both of these feats (and by 9th, the choice gets even tougher as to which feat to take), but if they can bank feats they can take them at 5th and 6th as well. If you are rolling up a 6th level Cleric, there is no disadvantage to doing so. The wizard will still have more feats, but they won't have more powerful feats.
Blech, I say.