I would argue against "deeper is better". My biggest and most recent pond is almost six feet deep. It seemed like a good idea at the time, but I now think it is too deep. The problem is I can't retrieve stuff from the bottom of the pond without donning snorkel and mask. A couple of large rocks fell off the edge of the pond into the abyss and they are still there because I haven't been motivated to dive for them. If my pond was four feet deep I could have and would have retrieved them. I think if I was doing it again, I would make most of the pond 2-2.5 feet deep with a small section around four feet. If you live in a severe winter area maybe deeper would be better, otherwise don't go overboard unless you like snorkeling.

We did the semi-built-in hybrid similar to what I think cathy725 is describing. We backed into that by accident. Were planning on a built-in and the cabinet is made to the specs for a panasonic built-in, but a month prior to our reno -- per Murphy's law -- our microwave broke. So we got a $99 kenmore to tide us over. Then when we realized this microwave would fit the space nicely and the cabinet has the required clearances for it (the microwave is smallish), we decided it would be better to do the semi built-in option. So we asked our cabinet maker to put a strip of molding at the top to give it the appearance of being more built in, but the interior dimensions are actually larger. We figure this gives us the best of both worlds. Lower up front cost by reusing our existing micro, ease of replacement if it breaks, and the cabinet is still sized for a built in if we ever decide to change our minds on that. But given our experience so far in the 14 months we've had this, I don't see ever switching back to a built in now. Here's what ours looks like. A bit hard to see the molding strip that makes it appear more fit-to-size, but the interior cavity goes up to the bottom of the frameless cabinet door above the cutout. Please forgive this grainy pic that makes the mw look horrible, it's not a high enough photo resolution to be blown up that big, but hopefully it gets the point across:

I'll chime in here. I have had mine in use about 7 1/2 years. They were brand new when we started looking and planning and I had a hard time the the price tag. As it turned out, using the drawer solved a lot of layout issues so we paid the $6-700 it was then, realized it was our east expensive built-in appliance, Sharp makes the best microwave ovens, and we figured the cost should go down by the time we might have to replace it and worst case we could put a small shelf unit in the space. Well, the cost hasn't gone down, I'm sorry to say, but I am not looking to replace it either. When I do, it will be with another drawer. I was pleased with how well we liked using it, found it had settings I didn't know it had and they worked well for us, and the keep warm setting gives me a second warming drawer for the craziest of times (actually used both for Thanksgiving one year when one guest was over an hour late). The drawer opening is so much better than having to bend down to see the flat front of a shelf unit or to reach in under your counter. Not having to lift out a steaming dish, set it down, stir and lift it back is so much easier. I'm tall and have bad discs in my neck, so that matters to me more than our other family members, but I don't think they'd want to change either. I'm coming up on 8 years in and I'm not going back. Point well taken about the cost of a micro plus trim kit of a built-in version that may not need the trim kit. And the only appliance you might get for less is a DW if you go basic. For a better, quieter model, you'll be in the same price range.

I'll add that you can see that most of these shelves really aren't that deep. Unless you're going to do roll-outs, things can get lost behind other stuff, never to be found again until past expiration, if you have a lot of deep shelves. You might have deeper shelves at the bottom for bigger stuff like that 30# container of flour or that flat of water bottles and such but you will want less deep shelves (10-14" max) for things like spices, seasonings, and canned goods. Shelves sized just an inch or so taller than cans are great for canned goods so you don't have to stack them. If you eat a lot of cereal, another shelf sized for the cereal boxes would be handy. So really think about what you want to store and where in your pantry you want to store it. Also consider adjustable shelving so you can change things up if your needs change or you have estimated your needs wrong. Also, even if you don't anticipate actually using appliances inside your pantry, you might as well wire a plug-in inside just in case you change your mind down the road. It would be easiest to do it while down to the studs already.