You WILL see minute cracks where the rails and stiles meet on an all wood door, as well as where the panel is inserted into those stiles and rails. That's just how wood behaves in the presence of moisture--including your wood floors. They too will gap in the winter and potentially cup in the summer. It can be controlled a bit more if you use AC in the summer and use a humidifier in the winter, but nothing on the planet will stop it. Choosing wood stiles and rails with MDF panel will stop most of the cracking at the joint where the panel meets the stiles and rails, but it won't stop the cracking where the stiles meet the rails. If the natural expansion and contraction of wood will drive you crazy then don't get wood. Get an all MDF door that is routed to resemble a recessed panel door or raised panel door or whatever you are looking at. And then choose thermofoil if you want a "perfect" paint job too. Because even sprayed MDF will still not be 100% perfect. It's about as good as you get for smooth paint, but thermofoil is smoother and more even still.

Anything involving wood will have some shifting of the wood. The MDF will remain stable. Having an MDF center will mean that part won't shrink and expand, but the wood frames will. I recommend it. Now, keep in mind that you're sitting there LOOKING for differences in the wood. And, you're seeing it in today's humidity, vs. all seasons'. Once wood/mdf doors are up, you won't be looking at it like that and even the minimal shifting of the frames won't be slapping you in the face. I think he's being straight with you and is on the mark giving you the options. It's not like he's trying to get out of work. Wood doors cost more, so he's looking out for your pocket and quality, IMHO.

Actually, I spent a lot of time last night reading old threads on our cabinet brand. It's the six square brand (6 Square- typing that so it can show up in future searches). And now I'm getting cold feet. I am definitely on a budget but if I knew I could get something better for a couple thousand more then I would do that. We are using a really great local kitchen and bath design place with a very long and trusted reputation so it didn't occur to me to wonder about the quality. Should I worry?

Then I would be going back to the kitchen designer and have them bring the issues to the cabinet company. I would assume you bought from a kitchen shop/designer representing that cabinet company. I purchased Wood-Mode cabinets from a long time reputable kitchen designer and I know he would be working with me if any issues like this came up. I paid the KD and not Wood-Mode, so I have to go through the kitchen shop/designer to resolve any problems. Who did you pay for the cabinets? Of course, if that person/shop is not helping you then I would escalate to the regional representative of the cabinet company and then up the chain of command.