Well they're not all the same Ganon. The reincarnations aren't going to be aware of any boy in green standing in the way of their goals (unless they bother to pay special attention to Hyrulean lore before they start trying to take over Hyrule).
I imagine most Ganons haven't faced off against more than 2 or 3 Links (if you only count FSA Link as 1 Link rather than 4).
We know that Ganondorf must have been reincarnated at least once, before FSA.
We also know that Ganondorf has been killed at the end of WW and TP. There are also theories that the "spirit" of Ganon is seperate from Ganondorf, (perhaps Ganon is only dormant inside of him?) and has appeared in his monster form multiple times.
Putting this all together, we do indeed come up with inexplicable returns of Ganon, at the very least, whereas Ganondorf's one return is explained. (He does have one more inexplicable return if you don't place ALttP after FSA). What we have so far supports the idea that Ganon can come back to life very easilly, (most likely through unknown ressurection rituals, as he needed one in OoX).
Honestly, though, I take the Zelda series to be full of symbolism more than anything, especially in it's characters. Ganon is just a symbol for the bad guy, the ultimate evil that many Links had to face. Until there is some sort of continuity in Ganon's returns, I don't think the matter can be explained fully. Unless you beleive his spirit is just straight up immortal, and "killing" him only banishes him temporarily.
Gannon has been dead for a LONG time. It's all about Ganon/dorf now. I think he keeps coming back because he got screwed over by the goddesses and it's his destiny to. Sort of like how Link and Zelda always have to defeat him. Even if I personally believe there should be a few times that Ganondorf wins, just to even things up a bit. I mean, sooner or later, one of the Link's or Zelda's are going to have to be evil.
I just have to say this because this is something that's been irritating the crap out of me.
Ganondorf is the only attractive male in the series.