If James is talking about player value from a GM's perspective (as he seems to be), then that value needs to be completely divorced from how the team as a whole performs. What a GM is concerned about is answering the question "How many dollars is he worth?", and the answer to that has nothing to do with how many wins the team has, or whether it has more or less than the Pythag estimate. If the Yankees' bullpen cost the team a bunch of games, does that mean they should pay Judge less? Of course not! Judge should and will be paid based on his own performance. It's not as if other teams have suddenly devalued Yankee players by 10%.
As for his five points, they also have problems:
1. "We don't know if clutch hitting exists"- As Tangotiger has pointed out numerous times, we need to stop with the binary thinking whereby something either exists or doesn't exist. Everything effects how a player performs, from their diet to how long they grow their hair. Therefor, the question is how much does it matter. In the case of "clutchness", it is part of every player's skillset, but the evidence strongly suggests that it isn't as nearly as big a factor as the people who talk about it suggest. So while it should be included in players evaluations for completeness sake, it isn't going to make a huge difference when talking about a single season (over a long career it will add it up).
2. "It doesn't matter whether it's luck or skill"- Of course it does. In order to properly assess a player's value, you have to figure out how much a player's stats are reflective of his skill.
3. "There is 'luck' everywhere, and sabes don't account for most of it."- WAR is solely concerned with how well a player performed, it is not concerned with why a player performed as he did. So ideally in-game factors such as umpires, opposing players, weather, etc. should be included in WAR, but health shouldn't because that's simply not what WAR is trying to measure.
4. "The connection between W's and stats is the only reason you do stats analysis"- True, but James' method of adjusting a player's value based on a teams win total is extremely ham-fisted. We now have detailed play-by-play data which allows us to measure how much a player helped his team win each game. There is no reason to be looking at a team's overall record when we have the info to grade every single pitch.
5. "What about a player with monster numbers in AAA?"- If James' is concerned only with how many wins a player contributes to a major league team, then he must think a minor leaguer is worthless no matter what his stats are. His own Win Shares system would assign such a player zero value.