Minimize pressure losses on interconnecting tubing and heat exchangers. All pressure losses equate to lost energy.
Properly designed inlet and discharge check valves: Pressure drop = energy loss and reduction in isentropic efficiency. Perform a proper dynamics analysis on your valves - note that valves operate at a peak efficiency only at a single RPM (sweet spot) which is dependent on the design.
Minimize piston ring friction: Ring friction creates frictional losses and also generates heat that can enter working fluid. Frictional loads are a function of dP across ring and dimensions of ring.
Minimize piston ring leakage: You don't want to compress twice. Proper ring design can virtually eliminate leakage, though you should still expect a few percent loss here.
Minimize auxiliary equipment and losses from oil pumps, water pumps, etc. This includes pressure losses for oil and cooling water flows.
Properly size flywheel: Pistons produce all the work during 1/2 the stroke. This can cause substantial fluctuations in electric motor RPM which reduces motor efficiency.
Don't loose product: since rings are generally segmented or have overlapping open ends, some leakage is to be expected. Low pressure packings or a sealed crankcase are a necessity for capturing and recycling process fluid.
Minimize oil slap and windage in crankcase. Aerodynamic losses inside crank are often an area of neglect since they are very difficult to accurately predict.
Optimize oil blow downs (for oil lubed compressors only): Some process fluid at high pressure is always lost during blow down which equates to lost energy and a need to recycle product.
etc...