The main limitations of CC are: You must have the latest version of DirectX 9 installed, not just 10, but we haven't seen any issues having both installed.
Then another is hardware acceleration, or rather the limitations with vram. While its great for multiple small instances, large textures simply eat it up, so a great deal of planning is in order.
You can't just pile on megabytes and expect great results.
I would say dealing with the quirks of the program is an issue, as I hear that repeated quite often, but the fact is you'd have stuff like that in any language, or engine.