Just like anything else, it has its pros and cons. As you pointed out, it can stain, and can be more difficult to clean up. Another downside is that it cannot be used with toys made out of silicone. But as the others mentioned, it is superior in slickness and how long it lasts. If you do try water-based and find that they don't last as long or don't lubricate as well, you should really look into hybrid lubes. I've personally used Wet Synergy Cool Tingling (also available in warming and plain) and loved it. You still need to be careful with silicone toys, but it's a blend of water and silicone. So it will be more slick and last longer than plain water, but will clean up easier than plain silicone.