A separate toilet for the boys, so that they can clean it themselves [bleurgh].
In fact, if I was building myself, with your lot, I would build four bedrooms (all exactly the same size), with Jack and Jill bathrooms between each pair of rooms - boys share one, girls share one. Cupboards and bathrooms between rooms also cut down noise from room to room. And I would have my own en suite they weren't allowed into.
Large laundry/utility/boot room with drying space for boots/sports gear/schoolbags etc. All entry and exit from house through that room, not through the front door. Stairs direct from that room to their bedrooms.
One big sitting room with enough seats for everyone, so that you could at least have some pretence at a family life .
No study - a big enough kitchen to have computer in the corner, so that you can keep a bit of an eye.
A playroom divided from the hall/main house by a glass wall with no curtains, to watch comings and goings of various boyfriends/girlfriends.
As you may realise, I've thought a lot about this. My house has three teens, but none of the above, I don't even have my own loo [cries].
Family computer room is good - our dining room is this most of the time (we eat in the kitchen unless people come over - so that you can keep an eye on their computer activities and also be in the same room for casual chats.