This isn't the best situation in the world, but it also isn't the worst.

The upside of the bulkhead is that there is no one directly in front of you for your son to kick. The downside is the lack of storage in front of you. In my experience, the lack of storage only becomes a huge issue if you can't get space in the overhead bins right above you or if you experience an extended ground hold or circling on descent. Otherwise, it's not horrid to get up and get what you need down, esp. with two adults.

In my opinion, since you are not trying to install a car seat, the immovable arm rests are a wash.

I personally would probably just go for it and leave things alone since you are together right now, but we've also done four hour flights to CA with a lap child older/larger than yours, so it comes down to what you are comfortable with.