5980 is expensive because:
1. Patek did not make a lot of 5980 initially because there was a problem in the new movement. They spent some time to fix it.
2. It is stainless steel (SS). Patek consider SS is a special metal in making watch. It is the Patek tradition. Therefore, they did not make a lot of SS watch and people in general are prefer to buy the SS Patek (because of its "rarity").
3. It is the first pure automatic chronograph from Patek.
4. A lot of people want to have a "Daytona" from Patek for a long time. 5980 is the PP's "Daytona"
5. The "3712" proved the idea that Patek complicated Nautilus watch can demand for a large premium. With the point 1 to point 4 above (and the "3712 event"), the market price of 5980 went up crazily.
5146 is less expensive because:
1. It is gold (or pt)
2. The annual calendar mechanism was announced more than 10 years ago
3. Patek made a lot of similar annual calendar watches (5056, 5035, etc..)
4. These annual calendar watches used to have deep discount 10 years ago (well... even 5 years ago)
In short, it is purely "supply-and-demand"....
5980 has much less supply than 5146
5980 has much more demand than 5146
So 5980 is much more expensive than 5146....
However, having said that, it does not mean 5980 is much better than 5146.... In fact, I would suggest people to buy 5146 first because it has a very "Patek" mechanism i.e. the annual calendar (and it is value for money).
Good luck.