It's a bummer they are keeping the base model at 16GB. It's pretty obvious that it's an intentional move to force people up to the 64/128GB models.
It's important to Apple's business to maintain margins. Taking down margins would be punished heavily by investors. So this move seems calculated to me to, yes, push more people to the $299 model. And to do that to offset the cost of more expensive components elsewhere in the device. We'll have to wait for a teardown to be sure, but that's my hypothesis.