We actually discussed this issue a little bit over here -- in that thread, poster after poster "confesses" to hoarding the strong recovery items in games like Final Fantasy, never using them. They're a wasted mechanic.
Players are leaving options like strong recovery items on the table, and favoring other ways of getting through challenges -- basically, grinding for power levels that allow you to ignore recovery items. The irony is that these same players might complain about the necessity of grinding.
From a game design perspective, one form of answer is to give players a behavioral "nudge" towards more interesting solutions to gameplay challenges, away from the boring path of least resistance. A case study from the RPG context: I've been playing Persona 3 Portable (which is fantastic), and often find myself reaching for powerful recovery items, including Soma, which is the equivalent of Final Fantasy's Megalixir. P3 takes a number of measures to make grinding less attractive compared to the alternatives: whenever you go into the dungeon to grind, it takes up in-game time you could be using to pursue social links; if you fight too much, you will be "Tired" the next day and face gameplay penalties; you can almost never grind safely, because easy monsters give hyperbolically discounted XP rewards, hard monsters are dangerous, and there are no save points to camp at, and out-of-dungeon recovery is expensive. These features tweak players' incentives and help them rely less on grinding and more on systems that might be neglected otherwise, like the recovery items.
It's fair to think about it as a difficulty issue, but more importantly not all solutions to a difficult problem are equal. If a difficult boss can be dealt with either by 1) grinding or 2) tactical use of recovery items, we might find that 1) is the default solution people will choose if allowed, whereas 2) might be much more interesting if players are encouraged to try it.