Cocoa is pretty good, but like all frameworks, it definitely has its downsides. Point #1, unfortunately, seems to be something that the author has a hangup about.

I find that using a single XIB for a view controller at a time works the best for me, and maintains some semblance of MVC. I work on a relatively large app, with more screens than usual, and I never find it hard to figure out view controller transitions or anything like that.

Same here. I think without Cocoa I wouldn't like Objective-C much at all.

I think it is worth mentioning that there is Cocoa and there is Cocoa Touch: supposedly saner and cleaner version. I am only familiar with the Cocoa Touch so I cannot compare myself.