At last getting round to a reply. Needed to work with something which hadn't been covered already...
yeah, OOT's ending is only a problem if you try and connect all the Zelda's together, when only a few were actually made to connect...
TP was the first game where the creators actually confirmed its placement in any form of timeline, and yet its ending left out this rather large plothole for the placement of games which could follow.
It's not about having your hand held and being walked through every detail. It's about some sense of satisfaction at a complete story. How did Link know it would be safe to remove the MS from Ganondorf's body? Is there some special Hyrule Morgue for dealing with potential kingdom-conquering villains?
Perhaps by leaving Ganondorf's fate open, it enables gamers like us to speculate and use our imagination some (a lot like the timeline theories everyone's so fond of posting about). So I put it in the same department as timelines.
Well in answer to that comment... Click here.
I think the real reason why possibly EA and certainly others who want Ganon excised from the series might be upset with TP's ending is that they wanted definitive proof that Ganondorf was destroyed for good (a la WW), that he would never come back, and so that he won't appear in the series anymore. There are many who want assurance that Ganon(dorf) will no longer be the main villain (after only a single bad appearance in all honesty) so that the Zelda franchise can metamorph along the path of a MM-type trajectory from here on out. When that assurance was not offered in TP, it suddenly becomes a sucky ending.
Just FTR, I'm more into Ganon taking a break than being completely removed from the series. I just don't mean the kind of break he took in TP though, where he's sat around in the castle doing sod all.