What's your decor style? A picture of your dining set would be helpful in guiding light choices. And pictures of your living room furniture, if it's open to the kitchen/dining area.

You really cant get help without letting us know what your style is. Your kitchen is a pretty blank slate and probably could go in many directions. Youre lucky, not too bad to live with.

I would suggest installing new recessed downlights for the main kitchen lighting and would suggest removing the ceiling mounted fixture. It's goin to clash with whichever pendant fixtures you choose. As for the pendants, that really depends on your personal style, the style of your kitchen and style of your furnishings.

personally I would switch the kitchen and the little hall area all to LED waffer lights you can get 6 packs pretty well priced. for the nook, I would pull from the stair railings and go black maybe with some gold. I think you need working light and buying pendants now for a kitchen you will gut seems like a waste, plus it will open the space up and make the island less of a focal point.

I am going to be doing that in my similar kitchen.