Pits suck because they are simply not fun. Multiplayer is primarily about roasting each other (simplified, obviously), not about navigating skills. If I want to play a game that focuses on the latter I'll go play a test. An example of pits used in a good way is The Warden Woods, where the pit is immediately obvious as such and falling in it is usually 100% your own fault. In most levels however pits are either overused to such an extent that it is hard to remember what drop is a cliff and what isn't, or simply not distinguishable from "normal" drops. This makes falling in one a frustrating experience because you get the feeling that the level is designed as such that you couldn't have avoided the pit anyway.

The difference between other factors that need to be "learned" in multiplayer and pits is that those other factors do not punish you when you are still unfamiliar with them. This is why I personally don't have a problem with warp-based pits such as in SILWIL, Extraterrestrials or Very Stupid Floating Castle, which can actually also be used to your advantage as a quick means of travelling to a certain place. Pits on the other hand obviously do punish you as you die when you fall in one, which is frustrating.

Making pits scream "hey! look! you will die and you will not like it! don't fall in me!" as suggested in the first post is actually a good idea, since in that case it is fully the fault of the player if he falls in them (and the player will know so himself). If the pits are not obvious, players will blame the level for not making it clear that there was danger in falling at that spot. It is irrelevant whether this feeling is justified or not.