Are taller landing gear bad for aircraft, particulary large airliners? Buiding larger engines for larger aircraft as opposed to smaller but many engines has proved to result in more fuel efficiency.
Having established one of the main drawbacks or impediments to building larger engines are ground clearance for engines in light of aircraft/airliners in their current under wing configuration. This configuration in light of current technological advancements seems to offer the greatest advantage in terms of control of the aircraft, stability and weight closest to the center of gravity when flying among other things. 

If space to store the retracted gear were not a problem due to some new design, are taller gear for airliners necessarily undesirable for landing and take off? Do they present some technical problem if for example they were strengthened, the extra length would present some problematic leverage problems as they get closer to the pivot and "load"?
Tall landing gear has been used in the past: 



The Tu-114 needed really tall gear to clear the really big props. The drawbacks are extra weight and volume, as described in the other answers.

The Tu-114 was so tall, on its first flight to the US (the prototype was used to ferry Nikita Kruschev to the UN for some shoe banging) the available boarding stairs weren't tall enough. That arrival raised some eyebrows in the West because they'd done a nonstop flight from Moscow (the Tu-114 was the first aircraft that made that possible).