Well, for one thing we've just seen what happens when a President can't get his nominees confirmed -- he just uses them anyway without Senate confirmation. So I really fail to see any way that the process promotes good governance. But more importantly, the process is just broken. The minority party tries to drag out the confirmation process, even of relatively uncontroversial nominees, just to chew up Senate time. Presidents nominate people to less-than-ideal positions based on their likelihood of getting through the confirmation process. From my perspective, confirming over 1000 people has lots of downsides and virtually no upside.
I'd be more inclined to give Congress fewer powers to stop appointments and greater powers to remove people that are clearly incompetent/corrupt/etc.
ETA: And just for a personal anecdote, I have a good friend from high school that just had a Senate-confirmed position in the Trump administration. This guy should not have been controversial at all. But it took many months for him to get his Senate confirmation. Because the Senate rule is that there can be up to 30 hours of debate on any nominee. And there was no way Mitch McConnell was going to use up 30 hours of Senate time just so he could get my buddy confirmed as the deputy secretary of some agency. So, like most nominees, he had to wait until Schumer and McConnell negotiated a deal about the amount of debate time, etc. Of course, meanwhile, he was basically doing the job before he was even confirmed. So how does any of this make any sense?