I would go with a walnut stain with a wood with small grain and no knots. This would be consider a modern look. Or mid century modern. Which is back in style. Cedar would be best over pine.

Get the professional sander guys in to repair the living areas and kitchen but don't go too dark with the stain as it will kill the lovely grain in the matai. I'm thinking a couple of tones richer than the timber knots showing in your photo, definitely no yellow tone at all. In NZ stepping on to carpet especially in a kiwi winter is so much nicer than a cold floor board shock!!! A nice area rug for the lounge and you're done.

I'm guessing you are from NZ (kiwi) :) The handy sanders did our floors - http://www.handysanders.co.nz/. They did an AWESOME job and are reasonable priced. I would definitely recommend.

A very simple layout keeping the floor space within the kitchen, the WIP takes up a lot of space with not much gain, The broom cupboard could be moved to the Laundry/entrance, narrow. If the wall has been bumped out to the eaves on the deck side giving an extra 300 depth to the kitchen you could make the island 2700 x 1200 and all drawers. The wall of narrow pantry will hold all pantry needs and more, no deep cupboards to dig into. cheers