Why do some of the widgets (Web Positve, Media Player" seem to have an updated look/feel to the controls but others seem to still have the old 90’s style?

All our widgets have been updated. Compare the look of Haiku with the one of BeOS.
We went for a style that brings some slight gradients, but without overdoing it. Some people qualify that as ‘90s’ or ‘dated’, but after 10 years of heavy gradients, now look at Windows 8 and iOS7: sharp and flat is again the thing to do, now.

Will we get to have the updated widgets system wide?

You provided no specific examples of “old” widgets.

Some software may draw its own emulated UI controls, in those cases we have no ability to fix them.