I look at it from the opposite perspective. You can get this awesome fully loaded car that competes with the BMW 5-series and if you opt for the 40 kWH pack you get to save $20,000.
The Leaf is like an Electric Nissan Versa. You can't even get leather seats. I don't know why anyone is comparing the Model S with the Leaf. They're not even in the same solar system.
That is very close to how I see it. Batteries are still very expensive, and Tesla's concept is to build a car of a class which is in a good relation to the cost of a long range electric car. At this time, a premium sedan.
However, many on this forum (including myself) are more interested in the "long range electric" part than in the "premium luxury" part. (I'm saying simply "long range" but depending on context this includes supercharging which extends the range further). The degree, to which it is important for our personal use, varies, yet in any case, we understand the ability of "long range" to be a requirement for electric cars to go mainstream. Plus, even if we could rent a car, we would like to do the occasional long trip without using oil again, in the "comfort" of our own car.
Although the 40 kWh option, with a range of 160 miles at 55 mph, has a better range (with home-charging only) than any other non-Tesla EV that I am aware of, it probably makes more financial sense, in terms of "how much do I get for my money", for someone interested in the "premium luxury" part, than for someone interested *only* in the "electric" part.
So for someone who is interested only in the "electric" part, and compares the Leaf to the 40 kWh Model S, things may look like a mismatch.
It needs to be pointed out that the Leaf doesn't make profit (yet), as far as we know, and that is even for a mass-production experienced company as Nissan is. Even with the tax credits, Nissan can only sell the Leaf, below profit, because it is a huge company (in comparison) selling lots of other "stuff". So even if Tesla wanted to, attempting to directly compete with the Leaf, at this point in time, would probably be Tesla's end of existence. In the unlikely case that Tesla would be able to manage making a small profit, it wouldn't be enough to make substantial investments, or to pay back the government loan.
So any comparison to the Leaf, from Tesla's perspective, has to be done with the future Bluestar. In other words, the 40 kWh option does not replace the "missing" Bluestar. Hence the importance of Bluestar, and the need for Tesla to be able to make the investments eventually leading to the ability to mass-manufacture at a price competitive in the mainstream market, coinciding with the corresponding battery price development.
To me, it all fits together. For Tesla, I haven't heard a better plan yet.