Actually, oddly enough it seems to me that much of science fiction is actually limited to a one-dimensional view of the solar system, much less a 2D view. The reference to Pluto is a good case and point.
Everyone seems to think of the planets in such a fashion that they're strung together along a (long) straight road such that to travel "out" of the solar system from Earth you would have to pass along each planet in turn. Who's to say for any given year which planet (if any) you'll pass heading outward (opposite the sun) from Earth even while staying within the ecliptic plane.
One may retort that this usage is just shorthand for each planet's orbit. But the problem is deeper than that. For one example, consider Tony Daniel's Superluminal. The entire series is about an inter-planetary war. The "geography" of the solar system is intrinsic to the plot - which planet can attack which, etc. And it's all wrong for the year of 3017. The book describes a group heading towards Triton for an attack with half the group "continuing on" to Pluto. Trouble is, from the starting planet during that year Pluto and Neptune are in very different directions (almost opposite).
With regards to the warp drive, the ecliptic plane seems hugely relevant. For any inter-stellar travel, just plan things for one (or more) midpoint stop(s) such that your final leg has you heading relatively perpendicular to the ecliptic plane of the destination star system. Then pop out of warp slightly beyond the ecliptic plane (presumably near your destination planet) to dump the energy.