Don't forget to deal with pressure changes in the aircraft. Give the baby a pacifier, nurse him, or give a bottle frequently. The sucking motion will help the ears to adjust to the pressure changes. (I worked several years in Taiwan and a couple in Hong Kong. The people moaning about a crying baby ruining their vacation really bug me. They seem to think that people are traveling across the Pacific with babies for the fun of it. No, it is usually for family reasons, or home leave or something else other than just for the fun of it.) Quite a few of the trips back and forth had infants on board. Some people could never figure out why their child was screaming. Duhh. If your ears are popping, the baby's need to also.
For your primary questions:
1. Unless you are really flush with cash, is 12 to 15 hours in a larger seat really worth a couple thousand dollars more to you? For us, the answer was no. I would rather be stiff from a crowded seat and have the money for other purposes. Likewise concerning buying an extra seat for the baby.
2. Definitely take the direct flight. The fewer going through an airport cycles you have to do, the better. Far more so with a baby than if only yourselves. Obviously, you will not be the only person getting stiff and sore, and everyone will have to make a restroom trip or two during the flight, so sometimes just to get up and walk around is acceptable and not thought to be strange.
Other thoughts: TSA sillies. Be certain on the limits of liquids for baby formula, etc., and normal other liquids. It can be most frustrating, to say the least, to have to throw away some things you really need to have because of TSA paranoia.
If your wife breast feeds relax and do it. She should dress for the sake of not being overly obvious or exposed, and carry some form of light blanket for covering if desired. If your seat mate (presuming 3 or 4 seats in the row) or someone else does not like her doing it, they can get over it. Do NOT let the crew insist she go to the toilet area to breast feed your baby. US law, at least in every state I know anything about has in their varying laws concerning the subject, say that demanding that you go to a toilet stall or room to nurse your baby is not permitted. They may need reminding of this. Breastfeeding also reduces the formula liquid issue. At least TSA, so far, has not found a way to object to a nursing mother's breasts being full.