How badly do you need storage space? If you're not tight on space, my preference would be to just have open wall space over the stove area. Either leave it open, add a few floating shelves, or better yet make the windows bigger, if possible.

If you do need the cabinets, I like option 1. I don't think it looks bad at all that the cabinets aren't all aligned.

I like your original plan with one row of cabinets. It doesn't look like there is that much space above the cabinets - just do a nice substantial crown molding to the ceiling. Less expensive too.

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Or, if you really like the look of two rows of cabinets, maybe do a statement hood.

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What comprises a statement hood? What is the exterior made of? The same cabinet exterior material? Does a mechanical hood occupy all the space inside that rectangle? Pardon me, I am new at this...

I've adjusted the elevation of the kitchen

You need more drawers in base cabinets.

Here are examples for you to view.

Why can't you do them like in your original plan but just TALLER? WHy the stacked look? Skip the stack.

If you go with the stack, you can alter the face of a over-hood cabinet to match the lines on the others if you think it would look better. Or you can raise the hood (or get a taller hood) so that the cabinet lines up with the upper chunk of the other cabinets. Consider a wider hood if you're going to raise it much more than standard so you still catch fumes.