FLC HAD ALT EXCURSION IN A LR-60 WHEN ENCOUNTERING MOUNTAIN WAVE ACTIVITY AND TURB NEAR DEN; CO.

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WE WERE INBOUND ON THE QUAIL 3 ARR TO APA. WE HAD BEEN CLRED TO CROSS QUAIL AT 16000 FT MSL AND 250 KTS. AFTER LEVELING AT 16000 FT MSL; CREW EXPERIENCED MODERATE TO SEVERE CHOP AND MOUNTAIN WAVE ACTIVITY. THE AUTOPLT WAS ON TURB MODE TO DAMPEN THE CORRECTION FOR COMFORT. WHILE CLBING THROUGH 16200 FT MSL; CREW REALIZED THAT THE WX CONDITIONS EXCEEDED THE AUTOPLT LIMITATIONS AND BEGAN CORRECTION INPUTS. CLBING THROUGH 16500 FT MSL; I REALIZED THAT MY SENIOR CO-CAPT'S INPUTS WOULD NOT RESOLVE THE PROB AND SELECTED 'OFF' OF THE AUTOPLT. I THEN ORDERED HE GAIN CTL OF THE ACFT AT 16700 FT MSL. (I WOULD HAVE TAKEN CTL AT THIS POINT.) HE OBTAINED CTL AND IMMEDIATELY STARTED A DSCNT TO 16000 FT MSL. I THEN EXPLAINED TO DENVER OUR SIT. STRATUS AND TINY CUMULUS CLOUDS WERE ENRTE. NO SIGNS OF VENTRICULAR CLOUDS. SIGMET 'V2' FOR OCCASIONAL SEVERE TURB BELOW FL220; STANDING UP- AND DOWNDRAFTS VICINITY MOUNTAINS WAS ISSUED; SO WE WERE PREWARNED. WE WERE FLYING CO-CAPTS ON OUR FIRST TRIP TOGETHER. NOT KNOWING EACH OTHER'S EXPERIENCE AND I BEING THE JUNIOR CAPT; MADE THIS A TOUCHY ISSUE. I WOULD HAVE TAKEN CTL AT 16300 FT MS. WITH ANY OF MY FO'S. I ASSUME THIS CAPT'S EXPERIENCE WAS LOW. CRM ISSUES EXIST WITH 2 CAPTS; AS YOU CAN CLRLY SEE. THE ONLY WAY TO CORRECT THIS PROB WOULD HAVE BEEN: IMMEDIATE DISENGAGEMENT OF AUTOPLT AND PWR LEVERS TO IDLE. FORTUNATELY NO OTHER PLANES WERE AFFECTED BY OUR WX INDUCED ALT ERROR.