Both are exculsive first party action adventure games and are of the best franchises on their systems.

Before I would have said Skyword sword easily but now that there are more PS3s out there I'm not so sure. And Twilight princess only sold 1.15 million more than Uncharted 2 if you only count current generation of consoles.

So which do you think will sell more by the time the holidays are over?

Considering Zelda will actually sell pretty well in Japan and looks like it will reach at least 800k preorders in Americas, I think it will outsell Uncharted over the holidays. Lifetime sales are another story since wii u will certainly cut into any potential long term legs the game may have, but over the holidays I think Zelda will sell 3.75-4mil copies and Uncharted 3 will sell around 3.25-3.5mil copies

Before anything, you should edit your thread title to clarify that this is is about sales, you'll thank me later.

First Week? Zelda

By the end of the year? Zelda

LTD? This is actually pretty hard, I mean, you'd think Zelda would have an advantage, but Wii will go down dramatically next year, and that could affect Zelda's legs.
Uncharted, on the other hand, has proven strong legs through this gen, but it doesn't seem that it will have that impact that Uncharted 2 has had, and this year some PS3 exclusives have failed to meet expectations sales-wise.

When Twilight Princess came out, the Wii had a userbase of zero. I bought TP for the Gamecube. I imagine millions did. This time, there is only Wii.

And don't quote me on this but I get the feeling that Uncharted 3 isn't going to have quite the same impact as Uncharted 2. Zelda will outsell Drake despite Uncharted's early release.

This Year is gonna be stupid, so I'm just gonna do a random guess of lifetime numbers.

EMEAA -
Uncharted - ~2.6 Million
Zelda - ~2 Million

Americas -
Uncharted - ~3 Million
Zelda - ~3.5 Million

Japan -
Uncharted - ~200k
Zelda - ~1 Million

Total -
Uncharted - ~5.8 Million
Zelda - 6.5 Million

 Your Americas and EMEAA numbers are on point. For Japan, I would say 150K for Uncharted and 700K for Zelda.