Actually, There have been many of these 'inconsistencies' throughout the Series. It has now been theorized by LOZ Historian and Myself that the Sages, Ganon, Link, and Zelda have been reincarnated thrroughout the Series. Considering that there are more than one of each and they all appear to co-incide with one another throughout, it is much easier and thus less a pain in the neck.

As for that decree About all females in the royal family being named Zelda, that decree took place centuries before LoZ. So it is most likely that LoZ Zelda is a 'grand' niece of AoL Zelda.

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I AM 'THE RENEGADE KNIGHT'!