2 years is a reasonable lifespan for L-ion. I doubt your wife did anything wrong at all.
There's a lot of folk wisdom regarding rechargeable batteries. Most of it is totally false. A lot of it comes from the days when Nickel-Cadmium was the most popular type of rechargeable; that changed in the late nineties when the prices on L-Ions came down enough to make them feasible for everyday applications. Ni-Cads are very finicky, and can be damaged if not fully discharged before being recharged (among other things). They also had and continue to have about double the lifespan of L-Ion, assuming proper care practices are observed, so I think people who are used to them expect their batteries to last longer than is really feasible.
The biggest factor affecting a battery's lifespan is usage. The very act of recharging a battery causes damage to them; thus, in heavy use scenarios (such as a student who takes her laptop to every class) the batteries will wear out much quicker than might otherwise be the case. While a case can be made that late-stage charging is more harmful due to the higher current and voltage flows to get that last 10%, it's my opinion that this isn't a significant factor. Furthermore, a laptop that is plugged in all the time isn't actually passing current to or from the battery very often -- typically, it'll pass a small 'top-up' charge to the battery about once a month, and that's about the extent of it. This behaviour is to counteract the self-discharge inherent in all battery designs (including alkaline).
The only compelling reason to be strict about full discharge/recharge cycles is memory effect. Memory effect is prominent in Ni-Cad, present but minimal in NiMH and non-existent in L-Ion.
If you do store your battery separately, be sure to take it out and recharge it periodically -- I'd say every six months or so should be good.
Fun fact:
Of the three most common consumer-level battery types, L-Ion is actually the most fragile. However, the battery does have onboard circuitry to closely monitor it's condition and prevent damage. This circuitry is one of the main contributors to the dramatically higher price of L-Ion over other battery types, and even with it in place it' a rather trivial thing for someone who knows what they're doing to cause one to explode violently (this was
referenced in XKCD ).