should it come flush with my cabinets?

This may be a matter of personal preference. A couple questions to ask yourself is; does a counter depth fridge have the amount of space that you would need inside? and if you choose something larger do you have comfortable clearance in the room? Function is very important in design, and this is a purchase most people will have to live with for many years. It does not necessarily have to be counter depth if the other factors are considered.

From my understanding the trim kit is required for proper installation of a built-in style fridge. I imagine that it doesn't feel like it sticks out enough free-standing is because for a built-in there is still air-space required to keep it from overheating.

As you can see my oven comes out more then the cabinets on both side of the fridge, my question is would it look bad keeping the fridge where it is flush with the cabinets or bring it out more? the trim kit isn't completed yet.

My dilemma is the pantry isn't flush with the oven either very frustrating...

pantry doesn't come out as far as the oven, but I have to fill in the hole between too of fridge and cabinets with something, thank you for the advice I'll post the new pictures