What style of animation, and therefore what workflow and tool chain, do you plan to use?
Something like Flash might be suitable for controlling many sprites on many layers moving around among fixed scenery and background sprites, but weak at controlling positions pixel by pixel and animating/replacing the sprites themselves.
Drawing individual frames, presumably with the help of lots of copy and paste in different image layers, is more flexible, more time consuming, and suitable for layered image editors like Photoshop.
As a third option, but many other possibilities and combinations exist, you could capture frames from a 2D game engine, e.g. Game Maker, with the advantage of high quality, easily authored but constrained procedural animations, tiling etc.