I've noticed in recent years that WotC and D&D peripheral designers seemed to be of two (or three) minds regarding the way PCs could gain access to abilities from other classes without multiclassing, ala "fine-tuning" or "tweaking":
1. Spend X, lose Y, gain Z.
2. Lose Y, gain Z.
3. Spend X, gain Z.
In the first and third examples, X is typically a feat that triggered access to an extra-class ability. No. 1 was most commonly found in Dragon magazine features -- expend a feat to allow the PC to swap out one existing feature (Y) for some other (Z). It is the most costly in terms of character development.
The second and third cases are cheaper and functionally equivalent -- a simple trade. No. 3 formalizes the swap because it requires the expenditure of a feat to gain a new class ability; No. 2 is more of an informal GM approval trade. These options were usually found in the hardback supplemental books (Complete class series or Unearthed Arcana).
As you move forward into Pathfinder design and plan for its flexibility, I'd ask that you please give primacy to one of these philosophies over the others and be consistent with your decision.
