I'd buy a set of both, I'm due in October and I'm starting with flanelette then moving to cotton when the weather starts to heat up. I've found that having both means that the beds cooler in summer and warmer in winter. You'll more than likely use both as winter will be back again in a couple of months. I picked up a set of flanelette from k-mart for $12 on sale but I noticed that Target has them on-sale till Thursday for around the same price, which makes them affordable.
Hope this helps,
Snoopea