Runge-Kutta is a good general purpose method for numerical integration, but is complex to implement properly in an n-body simulation (it involves more than just updating each individual body with an RK4 step, because intermediate values depend on estimated future locations of other bodies), and has some properties that make it less ideal for orbital simulation. Symplectic integrators conserve energy...for a lower order method, the error of any given step might be much higher, but orbits won't gain or lose energy over time as they will with methods like RK. With long timesteps, simulations using symplectic integrators get "wobbly" rather than exploding.
Sounds like the benefit of Encke's method is basically in removing the integration error on the largest force influencing a given body. Interesting, but sounds complex and prone to implementation mistakes, as well as requiring a fair variety of additional parameters that need to be tuned for good results.