I agree with the author. The cut scenes would have provided better character development for both Morpheus and Cypher, as well as some more motivating additional doubt for Neo and perhaps a better payoff when he realizes he is the One.

However, I think the whole discussion about canon is nonsense. For this, for Star Wars, and for everything.

Is anything Star Wars watchable after 1983? No. So why even talk about canon? Just watch the good stuff and ignore the rest. Is any Matrix movie after 1999 worth watching? Of course not. So why even talk about it?

In both cases, the original writers didn't respect their own material; why should you respect their idea of what the "real" story is? Life is too short for bad art.