Interestingly, there is a page about this, saying
No joke, no hyperbole, Sergio Leone‘s 1966 film The Good, the Bad, and the Ugly is my favorite movie of all time.
Hum, ok, same for me! But that's not the point, here it is
Tuco is probably going to shoot Angel Eyes, but he’s a wildcard, so maybe he’ll shoot Blondie to get the money all for himself. Blondie knows that Tuco’s gun is empty—which Tuco, and we at home, don’t find out until the end of the sequence—and also knows that Angel Eyes is very likely going to shoot at him.
We know that Angel Eyes is likely to shoot both Blondie and Tuco ; who is he going to shoot first? We don't have a definitive answer. It is a matter of opinion anyway.
(And I don't recall Leone talking about that point in the DVD special features).
So, in my opinion, Angel Eyes would shoot first Blondie, because
- He certainly thinks higher of Blondie than of Tuco (remember also the scene at the camp, AE vs Tuco, then AE vs Blondie), and he probably wants to get rid of him first, Tuco would be a bit less of a threat.
- Even though Tuco has his gun (unloaded but he doesn't know), the scene seems to emphasize a duel between Blondie and Angel Eyes (Tuco being passive until a gun plays).
- The images from the scene tend to show the direction of AE's gun towards Blondie (he is right-handed, so it's not a definitive proof).
There is also an amazing video on that page, that deserves to be watched. It shows how clever the movie is. (It's too bad Leone is not with us anymore to see it :-(