Yup. "Cost per user" strikes me as a very '90s metric, for lack of a better way to put it. It is an unfocused average. It presumes that the singular purpose of any acquisition is user count. This makes especially little sense in certain cases, i.e., the Facebook/WhatsApp acquisition, wherein a large proportion of the WA users are likely to be duplicative with FB users.
"User doing what?" is a decent start. But of course, we have a host of other considerations to ponder: technology, platform, integrations, competitive blocking and tackling, etc.
FWIW, I still can't wholly grok the WA purchase price. The price seems largely to have been driven by competitive bidding between FB and Google. Also a healthy sprinkling of defensiveness and fear, mixed with a dollop of "because we can." Factor in some "we believe our stock is overvalued, and as such, we will realize a discount on price correction," and I suppose you arrive at a figure that will end up south of FB's nominal purchase price. The one thing I can say is that Instagram looks likes a ridiculous bargain in retrospect, and especially in comparison.
That said, to whatever extent we do want to talk about user counts, it's worth noting some history. Around the time Facebook had an estimated $15 billion valuation, on the heels of Microsoft's advertising partnership/investment in 2007, Facebook had about 50 million active users. WhatsApp has 465M+. Apples and oranges, to some extent. But still. Worth considering.