As said above, boost is your best friend. Intake and tune won't overcome what nature is doing to you at those heights.
At sea level you have 14.7psi of pressure (absolute) pushing into your intake/manifold/head/cylinder.
Using the chart seen here:
http://www.engineeringtoolbox.com/air-altitude-pressure-d_462.html
You see at 6500 feet you only have around 11.5psi (assuming same temperature). A 22% drop! With fuel injection the computer can compensate to some degree with fuel and ignition timing adjustments so you don't loose 22% of your power. More like 18-19% by most online calculators. Either way it's a large loss and will continue to be so until you restore that lost pressure to the engine.
The pistons don't "suck" in air, it's movement just creates a void to let atmospheric pressure work it's way in there. This is why the GenIII and GenIV heads have much less "restriction" than the old small block V8 heads. They make the flow path from outside into the cylinder much easier... meaning less pressure drop and therefore larger mass of air entering the cylinder. But it's still dependent on what outside pressure is acting on the engine. You will see a close correlation to the lb/min of fuel you are burning and the power you are making.
BTW: superchargers are more affected by altitude than turbochargers (the reason most WW2 supercharged aircraft had multi-speed transmissions in the superchargers). At any impeller speed and pressure ratio (hint: outside pressure versus boost pressure in the manifold), a supercharger will only move a certain lb/min of air. Since a turbo's impeller speed isn't mechanically linked to the crankshaft it will naturally spin higher in response to compensate. Not fully, but a lot better than a supercharger. Most superchargers spin in the 50-80,000rpm range. 130,000rpm isn't uncommon in a turbocharger. And just like for an engine, shaft rpm means potential. Anyway, off topic. Sorry.
Intake and tune will help, but won't get anywhere near compensating for the altitude difference. Even the mighty 6.2 vortec will feel a lot more lethargic at those heights.