Let's look at the Pack Rat perk to illustrate.
The posted requirement for Pack Rat is 70 Barter. I think Barter is an absolutely great prerequisite. Why? By increasing your weight capacity through Pack Rat, you are going to be toting a greater amount of salable items. That high Barter requirement for Pack Rat is going to pay off when you go to a store with all that extra stuff to sell. Many times over. Stim packs, repairs, and a dozen other items are going to be easily obtainable.
Some of the posters here said that they'd prefer it if perks had an either/or requirement, like in Cowboy. However, if you look at what Cowboy enhances (short-range weapons and melee attacks), it makes absolute sense. Cowboy would not be such a hot perk for a long range, combat-based character.
Anyway, I think people need to look at the less-obvious benefits these perks bring to the table.