From what I've seen of Apple's strategy with the iPods and, to a some extent, with the Macs, they seem to be marching steadily towards one goal: eliminate any reason for not buying one. With the iPods, this meant a steady stream of newer, smaller models to counter the "but its too expensive" crowd. With the Macs, Apple has bent over backwards to remind people we still run MS Office and we've got a ton of even better native apps too (plus Apple caved in an started giving away Boot Camp, the ultimate offer of appeasement).
If Apple feels the lack of Skype is a real reason people aren't adopting the iPhone in droves, then Apple will definitely do something about it. Personally, I see them working on the price/size issue first. Apple could probably make a pretty good impact on the phone market with a more traditional candybar phone without all the web-browsing/video iPod features. Sort of an iPhone nano at about $199. Maybe they could even strip out the cell phone bit and go wifi-skype all the way! 😀