I have the same problem since I ride a 42cm cross bike. I use a full size bottle on the downtube and I bought a small wide mouth nagalene bottle for the seat tube. I generally stash my energy bars and snacks in the short one and use the other for water. If I'm doing a long ride I use a hydration pack.
Check out girlbike.com. Crystal also had the same issues and switched to side mount water bottle cages. I've recently seen ones that twist sideways so you can get the bottles out too.