Shape of planetary orbits What makes Venus' orbit almost circular, though mercury's is highly elliptical,even though it is closer to sun ? Further, Why is mercury's orbit most elliptical right after Pluto ?
 A: All these trajectories are solutions of a  many body gravitational problem. In reality they approximate ellipses and spheres, because they perturb each other's trajectory due to the gravitational attraction among them. The real solution can only be found numerically, as it is done for planetaria .
So it is only to first order that the differences in the trajectories of the  planetary bodies can be compared. The first order answer to "why these differences" is "because the boundary conditions on the formation of each planet were different, so the trajectories will be different". This moves the goal posts to "why were the boundary conditions different" which forces to look at a specific model of the formation of the planetary system. For example 

According to the nebular hypothesis, stars form in massive and dense clouds of molecular hydrogen—giant molecular clouds (GMC). These clouds are gravitationally unstable, and matter coalesces within them to smaller denser clumps, which then rotate, collapse, and form stars. Star formation is a complex process, which always produces a gaseous protoplanetary disk, proplyd, around the young star. This may give birth to planets in certain circumstances, which are not well known. Thus the formation of planetary systems is thought to be a natural result of star formation. A Sun-like star usually takes approximately 1 million years to form, with the protoplanetary disk evolving into a planetary system over the next 10–100 million years

So there is a lot of modeling space to get different boundary conditions for different segments of coalescing matter about the new star, and be able to model the final state differences in the planetary trajectories. 
