What's wrong with using preferences for everything?

Preferences don't compose. Two modules that both preference the same class can't coexist, whichever loads later wins, and the loser's logic vanishes silently. In a Magento store with 30+ third-party modules, this is roulette. Plugins compose: ten modules can around-plug the same method and they all run, ordered by sortOrder. The fix: 90% of the time you want a plugin, not a preference. Reserve preferences for: replacing a non-public method, overriding a final class, or changing constructor signature. And even then, prefer a virtualType + plugin first.