My thoughts, based in part on being a T&FN subscriber for over 30 years. Some of these items (in no logical order; just writing them down in the order I think of them) have been mentioned previously by others, but there's no harm in repeating:
1. T&FN doesn't include indoor marks for rankings for events below 3000 (and not for 3000 either, I guess, since I don't think they do 3000m rankings anymore), so Manzano's win over Centro at USATF Indoor doesn't count.
2. They don't include road marks, so 5th Avenue doesn't count.
3. Makhloufi's 1500 win in Oslo was a B race over a very weak field, so it means next to nothing.
4. Makhloufi had a fairly limited 1500 campaign; just 8 finals and only 2 Diamond League meets (in which he placed 5th [Monaco] and 8th [Brussels]).
5. Brussels was the Diamond League Final, so probably had the 2nd most weight after the Olympics. Kiplagat and Gebre went 1-2.
6. Sometimes no one dominates an event, and so no one really "deserves" to be ranked #1, but someone has to be!
7. Sometimes when the medalists in the biggest race of the year, in this case the Olympics, have otherwise such mediocre seasons, it doesn't carry as much weight when it comes time to figure out the end-of-year rankings.
8. Manzano had a truly lousy season other than the U.S. Champs (which doesn't mean much on a global level, other than the fact that he beat Centro) and, of course, the Games. He competed in 5 Diamond League meets, and his placings were 12th, 11th, 10th, 11th and 11th.
9. I can see RoJo's point about Makhloufi possibly deserving the 3rd spot ahead of Gebremedhin, but the latter ran 6 Diamond League meets, and had solid placings of 7th (Doha), 2nd (Pre), 3rd (Oslo), 2nd (Lausanne), 1st (Birmingham) and 2nd (Brussels). He ran okay at the Games (6th), so that body of work was probably enough to give him the nod over Makhloufi.
10. As others mentioned, time is the least important factor.