If they did this in order to fix conflicts between OoT and LttP, they didn't do a very good job. The Hylian Knights were defeated during OoT, Link being their last hope. There would be no one left to help the Sages seal the SR after Ganondorf gets the Triforce.
I completely agree. With our current understanding of this new branch of the timeline, the reasoning behind it just feels rashly duct-taped together. There's too much room for conjecture as solutions to incongruencies.
Even more of a problem, LttP states that the Sages weren't able to find the MS or a hero to wield it.
Did it really state that? It's still my favorite game of the series (oh the power of nostalgia), and I confess I haven't played it in years; but I have no memory of the game making that statement. I'm not doubting you though, as it feels right despite my gappy memory.
Reading that statement did provoke an unbidden idea though. 'The sages weren't able to find a hero to wield the MS' sounds almost like saying that they couldn't find a player to 'be Link', who Nintendo perpetually describes as a character that is blank slate designed so as to be 'us'. That could potentially then be further interpolated to mean the 'if' or 'Failed' timeline split is caused by the player failing to play OoT. So if you did play OoT then both the AT and CT follow; but if you didn't play OoT (mind boggling as it is, there are people out there that haven't) then the FT follows.
Now immediately that sounds like a sloppily foolish idea for the same reason that the Link being defeated in Oot creates its own timeline. If it happened in that game, it could happen in every game, and there would be nothing to prevent a failure (or lack of being played) based branching timeline occuring for all the games.
Still though, for me the idea that the 'failure' is merely caused by the player never having played OoT sits well in my head. I don't find it as objectional as Link actually being defeated, and it doesn't require the same kind of mental squirming that the debatable 'abandoned timeline' demands (as it always winds up being just two timelines when I really do the math).
The 'was not played' idea also works from a marketing perspective as well, in that OoT is the flagship Zelda game for Nintendo. Even with the awesomeness of SS and some of the other games, it's OoT that bears all the fantastic press of 'the best game of all time'. OoT was also the first game to be cohesively placeable in the timeline of the games, and is used as a North Star in all other games' placement (eg. SS was constantly referred to as a 'pre-quel' to OoT). I've even heard it dramatically said that 'the gaming world is split into two categories, those who have played Ocarina of Time, and those who haven't'. By creating a timeline based off of a player's lack of involvement, Nintendo would be enticing those that have played other Zelda games, but not OoT, to try out their flagship game (newly released on the 3ds). Additionally, by sequestering all the oldest, most contrary, and most unrecently played games into the 'FT', it allows the other timelines to exist freely for newer players who would otherwise only investigate the older games out of niche curiosity, and thereby feel little loss to the possiblity of Link 'failing', as they've presumably already succeed in preventing that outcome.
On another semi-coincidental but interesting level, ALttP, LA, LoZ, AoL all came out before OoT, and ergo the player couldn't have played it yet, thereby allowing for the Failed Timeline to be the primary one. The Oracle games don't really work with that though, as I think they came out briefly after OoT; but as they're already sequels to ALttP, I find that forgivable.
It's not a perfect solution, and still doesn't really give an adequate reason for the relavant 'timeline creating failure' originating in OoT rather than any other or even all games; but I still find it easier to digest, and the added 'flagship game marketing' adds another (slim) reason to add a timeline split onto OoT rather than one of the less world reknowned games.
That said, tomorrow NoA could announce that the failure was created by Link choking to death on a magically nafarious deku-nut.