I think I understand what the OP is asking. If I've got your post correctly, I think Ganondorf doesn't go straight after Link because he needs to make sure he gets all three pieces; this is why he bothered to capture Zelda after Sheik explained the importance of the Triforce to Link, such that Link would race after Ganondorf because he knew that Link would come and try to rescue Zelda, because then he would get the Triforce of Wisdom. What Link doesn't realize is that this is how Ganondorf is going to obtain all three pieces in one fell swoop, by defeating Link and Zelda in the final showdown, and obtaining all the Triforce pieces. This was the only way he could be certain that he would get all the Triforce pieces without any complications, because he knew that it was not only Link's destiny to stop Ganondorf, but also because Zelda actually told him to. There are several forces pushing for Link to go fight Ganondorf; if Ganondorf took the Triforce of Courage first, Zelda wouldn't rush in to get it back because she'd be much more cautious and less predictable.
If you're referring to after OoT, Ganondorf can't obtain the final Triforce piece (Courage) because the Triforce seemed to have been shattered when the Hero of Time brought it back with him to the child timeline, creating a time paradox. This is why the Triforce is shattered in WW.
Not to mention, there's always some sort of emphasis on obtaining all the Triforce fragments at the same time, hence why Ganondorf, Zelda, and Link are all engaged to some regard in almost every final battle where the Triforce is split.