I would've thought the struggle we've had in replacing him would indicate both how good he was and how difficult it is to find someone better. Much in the same way it would be for Mkhitaryan.
I don't think your perceptions really stack up to the evidence, personally. So in that sense I think the comparison to Mkhitaryan makes a lot of sense. Despite evidence from multiple sources that Nani was in fact good enough to not only be part of the squad at that level, but play an important role in the team, the nature of his game made it impossible for some people to acknowledge that.
Mkhitaryan and Nani are frustrating players. They take risks, they make bad decisions, they have flaky mentalities. Those particular traits act as an emotional trigger which prevent some people from acknowledging their overall contribution. Frustrating doesn't in reality mean bad, but for many they become synonymous. That's quite a flawed way of judging an attacking player in truth.
In 2011 we won the league and reached the CL final, beaten only by one of the best team's in the history of the sport by one of the finest performances in European cup final history. Nani was an essential part of the team that season. In the league he was nominated for young player of the year by the PFA, he was ranked the best player in the league by WhoScored, and he was widely acknowledged to be in our top three alongside Rooney and Vidic for the season overall. The
players obviously thought so. Here's how he was described at the time in the media:
And here's how he was described by his manager...