If you're trying to get more altitude for a specific aircraft, then you're pretty much talking about rewriting the entire flight dynamics. If it's a jet, it's probably not that big a deal. I'm guessing you can increase the max thrust, then fiddle around with the lift properties. For a piston pusher, you're also talking about making changes to the turbo or superchargers, or even adding them if it's currently a normally aspirated engine. Then, of course, you'll need new gauges to match all this if you're a reallism stickler.
That's just my slightly edjumokated guess...