Younis Khan is comfortably a better batsman than Pujara. You can apply a lot of filters/metrics, and Younis would come out on top. Forget for a moment that Younis averages more and has been more consistent. You and others have brought up impactful innings, and right away I can think of at least 5+ innings of YK where he turned the match 180 degrees around with his clutch batting with some highlights being vs India - Bangalore 2005, chasing 300+ against Sri Lanka in 2015/(16?), against England in 2016 in the final test winning Pak the match and drawing the series.
I can't imagine anyone, including Indian fans, would pick Pujara over Younis Khan unless they knew the series was in Australia, because Younis Khan will score more runs, win more games, play better when the chips are down, and turn games on their head in the 3rd/4th innings.
Sri Lanka, 2015: the pitch had completely flattened out by day 4 and 5 and Sri Lanka had a rookie spinner. Herath didn’t play that match.
You can gauge the level of difficulty when a player like Shan Masood scores 120+ in a fourth innings run chase. They were not traditional 4th innings conditions. In fact, it was the complete opposite.
Younis was actually the main culprit why Pakistan did not win the series in England. In fact, it was Pakistan’s golden opportunity to win a series in AUS/ENG/NZ/SA because it is not going to happen in the near future.
Younis was a walking wicket throughout the series until the Oval Test. Pakistan were practically playing with 10 min in the first three Tests.
They carried him to a win at Lord’s and we got battered at Old Trafford. In the third Test, at Edgbaston, had he turned up in either of the two innings, Pakistan would have won the series.
After failing all series including averaging 4 in New Zealand earlier that year where he played like a number 11 and scored 16 runs in 4 innings, it was no big deal that Younis finally managed to play a big knock on a perfect batting wicket under sunny overhead conditions.
He was long, long over due because he had been a complete disaster on the New Zealand and England tours until that point.
The Bangalore innings and the 147 at Eden Gardens in the previous Test were wonderful knocks, and they turned his career around. He was on the brink of getting dropped after Mohali and who knows if he would have ever managed to make a comeback.