Do you know the child seat policy of the airline you’re flying with? And what sort of child seat are you wanting to use; will it be rear-facing or forward-facing?
As others have said, most airlines usually require child seats be placed in window seats for safety reasons, so there is the possibility of not having a choice about the layout.
That said, in our experience, some airlines accepted a car seat in a middle seat in some circumstances. It’s best to check the policy of the airline before flying (even if you can’t find it on their website, it’s likely worth calling the airline). Also, you may want to consider having a copy of the airline’s policy on child seats to hand (on your phone or printed out). In our experience cabin crew hardly ever know their own airline’s policy regarding car seats, but most will be fine if you have the policy to show them and if you can point out the FAA approval sticker on the child seat.
Should you have a choice about which seat you can install the car seat, the direction it is installed (rear-facing or forward-facing) will also be quite important. We traveled with our daughter in a forward-facing car seat (Britax Frontier) until she was 13 years old, and when we had the choice she always preferred being in the middle seat. While clearly more comfortable and safer for her, the car seat did mean she was a bit higher and further forward than either of us and not able to lean forward, so when she was in the window seat, whenever she wanted whichever one of us was in the aisle seat, she had to ask whoever was in the middle first which wasn’t very practical. Also, being in the middle meant she could more easily reach the drinks or food herself when they were handed out, which was a bit awkward when she was in the window seat.
If you have a choice, and are planning on having the car seat forward-facing, we would suggest the middle seat if possible for the reasons above. However, if the car seat will be rear-facing, then it might be a different scenario as it’s probably much harder for an adult in the window seat to get around a rear-facing seat than it is to move around a forward-facing seat.
Another thing which might be worth thinking about is the “footprint” of the car seat. If it’s under 16 inches wide at the base, then it should not encroach into another seat, however some car seats have wider bases which can overlap with other seats. Depending on this, it might be very uncomfortable for some people to sit beside the car seat. If you were to install the seat in the middle, and the base of the seat is wide, then it will affect each person either side of the car seat, whereas installing it in the window seat means only one person would have to adjust for the base (although there might be a need for the person in the aisle seat to adjust to the person in the middle seat!).
Obviously it's different with a two-year old, and it’s been a while since we last flew with a car seat, so the policies and practices might be different now, but hopefully this helps in some way.