Yes, "best" protocol type questions without any sort of qualification are terrible (like this one? :P) as you can't definitively, objectively evaluate how good the answers are.
I would rather see questions of the form "How can I do X [with|without|using] Y?" (perhaps X="minipreps", Y="noxious chemicals" for the classroom miniprep question). They are inherently better questions as they will focus the discussion (such as it is on SE) on the core issue, so answers can address it and voters have specific criteria to judge them.
This shouldn't be taken to the extreme or you'll get questions that shouldn't have been asked in the first place as a much more basic, overarching question was excluded ("What kind of spark plugs should I buy so I can run my car on diesel?").