1. There's a gap between the upper cabinets and the ceiling. But doesn't look I can move the upper cabinets up to fill the gap because there might be pipes behind the wall above the cabinets...

That "gap" is called a soffit, and it very likely does contain pipes or vents of some sort. The easiest thing /cheapest thing to do is to add thin wood + fake doors on top of the soffit so it'll register to the eye as "more cabinets" but will really be fake. If you want "glass front look", consider going with mirrors in the middle of the fake doors -- people won't see their reflection up that high, and it'll look like glass doors. Fake doors will cost significantly less than adding cabinets, and cabinets that far over your head would be of questionable value anyway.

2. Will it look weird if I keep the left side of the cabinets but stain it to a darker walnut color but repaint the main cabinets to greige or light grey color?

Yes, that would be weird. And you cannot go with gray -- unless you also change the tile floor. Gray and tan are not friends. Are Not Friends.

3. what color of countertop would go well with the stained cabinets and the greige cabinets (if we decided to paint them greige or light grey)

Ideally your floor and counter tops will relate -- not necessarily match but relate. A simple white counter top would probably be best. Solid white isn't exciting, but it goes with (practically) everything and stands the test of time. If you want something more exciting, everyone loves TajMahal quartzite -- but, oh, the price. I personally wouldn't do that unless you re-do the whole kitchen and fix its other problems.

4. What color should the floor be? I am thinking checkboard with light grey and beige...

First, consider that removing tile is Real Work. If you can live with what you have, you might be happy later.

I love checkerboard, but -- again -- Just Say No to Gray. Its 15 minutes are up, and it will never play nicely with beige. Consider white or cream + tan checkerboard -- it's "softer" than the expected black and white.

And be careful with checkerboard. While lovely and classic, it is bossy and loud -- it demands to be the star of the show. If you go with checkerboard floors, everything else should remain simple, calm, quiet. If you try to put in "too many stars", they will compete for attention, and the result will be bloody eyeballs.

Sorry, that was a bathroom, but the point is the floor.

Definitely choose your floor and your counter top together -- again, they should relate.

5. Will I be able to fit a stand alone island (those ones that look like a table instead of the typical island.

Without seeing the measurements, I feel 90% sure the answer is no. I know islands are "the thing", everyone wants one, and -- when done right -- they can be very functional, BUT you don't want "island at any cost", which means cramming an island in where it just can't fit. Even a stand-alone.

6. Can I install a range hood above the stove instead of the microwave. I would like to install one that can exhaust outside, but the stove looks like it's kinda far from the exterior wall.

You can vent it directly up through the ceiling (well, do you have a second floor up there?), but it will cost Real Money. This is a function of the kitchen not being on an exterior wall.

7. What to do with the stand alone fridge, should I add a little cabinets on top and extend the cabinets on the side so it looks like it's part of the kitchen?

I agree it's a problem. Without seeing a floorplan and measurements, I'm gonna say you could remove some cabinets /move the dining room door to the right ... then add cabinets against the back walll /make the refrigerator a part of that cabinet run.

This would be an improvement, but -- again -- Real Money. Howevever, you have no appliances in that area, so it's not as bad as it could be.

8. Should I move the fridge closer to the window so I can make some space for the stand alone island?

No. That's trading one problem for another.

9. Will changing the main cabinets to shaker style a better idea? But then will need to change the left side as well to make it consistent.

Changing the cabinet style will make the kitchen look different but not better, and it would make no difference in the function of the kitchen. Work on function /layout first, THEN looks /style.

What's up with that one mis-matched cabinet?

I would leave it as is until we can rework and replace.

In a perfect world, I agree. But if you just HAVE TO HAVE A CHANGE, consider painting the cabinets yourself. It'll take you forever, but it'll give you a lift until you're ready to really re-do.