But your wife is one use case. Think of the users of SMS or email or any asynchronous communications protocol as a Venn diagram. You have categories of people who need to communicate with each other that happen to both have iPhones. Others both have GChat. Others both have BBM. Still others happen to be online for real-time chat at the same time.
All of these users fall into one umbrella category, however: a group of at least two people, at least one of whom needs to say something to another person. If I need to say something now to a friend, I use SMS ten times out of ten. Why? Because I know, without a doubt, that if I send an SMS, it is going to be read by that person regardless of device, software, etc. A centralized protocol is required to tie together disparate software. The 140 byte limit is annoying. But what happens when technology catches up to human length requirements, and it is extended to 400 or 1000 characters? Then you are going to care about length limits even less.
The author's point is that email as a concept and prototype is not broken and is functioning exactly as it should be, which is why it is the preferred communication medium for most people despite decades of development in better chat/list/calendar clients. Knowing you can get a hold of somebody every time is a benefit that outweighs any other. Same reason Skype hasn't taken over cell/land line phones. Centralized protocols are a necessity. Do they come with limitations for some use cases? Of course. Nothing can be everything to everybody. Which is why the author's point is so well taken: that additional functionality catering to single use-cases belongs at the client level in the form of extensions.
Edit: Also, it seems strange to me that people argue that email is broken because their inboxes have turned into todo lists. I think the reverse is true and people are looking at it through the wrong end. Email is such a simple, useful tool, that people not only use it for its intended purpose (communication) they now also use it for managing todo lists. After all, there are boatloads of todo list software and more and more coming on the market everyday, and yet people still use email while they talk about how shitty a solution it is.