Like almost everyone else, I chose Agriculture and Mining because they are the most versatile; they are useful in any start.
If I don't start with Hunting and don't have a camp resource, I often ignore it, as it's not really very useful. Starting with a scout is nice, but that's only a small benefit, and it can sometimes even be worse than a warrior since scouts are weaker and more vulnerable to animals/barbs.
Mysticism isn't necessary to start with unless you are trying to found an early religion, which isn't very useful anyways.
The Wheel is useful, but it's also something that's not necessary to start with. I'd rather be able to improve a tile but not have access to the resource, than have a road on the tile but not be able to improve it.
Fishing is obviously very helpful in coastal starts w/ seafood, but not so helpful when starting inland, so it's not as versatile as Agriculture/Mining.
Agri and Mining allow you to handle almost any start. You are coded to start with a food resource, which, if starting inland, is very likely to be a grain or livestock. Agriculture allows you to farm the grain, or if you have livestock, leads to AH. Mining allows you to improve any gold/silver/gems you have and leads to BW which is necessary in many forest-heavy starts and an important tech overall.