Blending Up Is Hard To Do
I would assume that the effect your referring to could be caused by
1) Accessing the hard drive to load the preset to memory - Solution: use a ramdrive program to put the whole winamp directory structure in your physical ram, this eliminated "pauses" when load the next preset
2) When MilkDrop is blending two presets it's have to do twice the work. The only thing you can do about this is to not use heavy duty presets (as you mentioned), or upgrade your system (CPU and/or Video Card).
I'm running DDR333, Athlon 2100, and a Radeon 8500 LE with 128MB memory. Milkdrop is set to 800x600, 512x512, and 24x18. Normally everything runs at 60fps, but occasionally it will drop. There's only so much you can do about that.