had they begun life sharing a room it probably wouldn't be such an issue. My kids have separate rooms, and CAN NOT take naps together, because they think when their together it's just like any other normal time during the day...time to play.
You might be better off having the baby and the 2 1/2 year old share because if the baby goes down first, there won't be someone moving around making noise when the 2 1/2 year old goes down so it may easier for him to be restful.
Plus, 4 years is quite developmental gap in both cognitive understanding and responsiveness.
I am not sure I'd try such a radical switch when such a big adjustment is coming. It'll be hard enough for your 2 1/2 yr old. so I am sure you want to decorate and have a cute girly nursery, but you could still make it generically cute and even create a special area for you son. Like maybe a tent-like bed.