They lowered the prices on the SKUs to compensate.
Honestly, there's no pleasing some people. When the pen was included, everyone was saying, "let me buy a cheaper SKU without the pen; I don't want it!", and now that they've done that everyone is complaining.
I got mine for the equivalent of 1028 USD: SP4 i5, 256G, 8GO pen and type cover (this was a special offer though). This was one month ago. So when the new model will go out, the prices of SP4 will probably drop.
So far the only drawback of the SP4 is the battery life, so except if they improved it a lot I don't see the point of paying the 500-600$ more. They say it's possible to watch 13.5 hours of videos, but manufacturers tests are not trustable anyway. It would probably be more like 7-8 hours of real-world usage. Are the extra 3 hours worth the difference? Maybe, but for my usage no.
Yes, it is why I said "Maybe" :-) I'm actually working in research and I'm going to conferences, but the limit of ~4 hours kind of forces me to focus on talks instead of coding all day long.
I mean, during the conference day I'm kind of depressed of not having battery any more, but with cold head I tell myself it is better for me.