On my long AT section hikes, I did all resupply via USPS Priority Mail. I use ziplock bag cooking rather than using my pot to cook foods. That allows pre-portioned, individually ziplocked meals. But its a big hassle in preparation, and it put a big load on my wife to get the boxes ready and mailed.
The issue I have with resupplying on the trail, from grocery stores, is that you have to live with what's available. You either repackage foods or live with carrying extra packaging waste; you use valuable town time shopping and repackaging; foods can cost more; and you may end up carrying significant extra weight. And if you do ziplock food cooking, you'll have to carry extra ziplocks or throw away some of the ones you pay for.
If you mail, UPS, or Fed-Ex boxes, you can plan to meet your nutrition needs when you have the time and energy to spend on planning and food acquisition. By the way, a few of the resupply locations on the CDT do not accept USPS packages.
Well, I still want to plan ahead, address nutritional needs, and send boxes to resupply points. But I also want to make the box preparation as simple as possible. This time, in place of individual meals, vegetables, fruits, and snacks, I plan to bag each type of food for the full resupply period, and include empty ziplock bags as needed. I'll portion it out on the trail. Finding a desired food in the food bag is always an unexpected hassle--sometimes I have to pull out almost everything to find a food at the bottom of the bag. Presumably, this approach will make it easier to find the foods on the trail.
And more importantly, it should make boxing easier, and hopefully reduce volume. I know some people blog that they complete 28 boxes or so before they leave. I'm not sure how they tailor that to unexpected trail conditions and less or more miles and days than expected. If they change their alternate/official trail choices while on the trail, that can also very easily change the number of days a box (or boxes) would be expected to support.
I'm working my food plans now. I've never had hiker hunger on the trail, though when I get to towns I don't seem to have any problem eating way more than usual. So there seems to be a limit on the number of calories I can carry and expect to eat. And it will result in a significant calorie deficit. Protein is another issue. I plan to carry whey isolate to create a flavored protein shake/drink. I'll use vitamins of course to try and avoid vitamin and mineral deficiencies.
Variety is something I work pretty hard at, but there are limits imposed mainly from cost and prep time. I hope to mix Mountain House dehydrated meals with minute rice, ramen, and mashed potatoes. Probably half freeze dried and half of the quick carbohydrates each for the resupply. I've also got freeze dried vegetables and fruits that I will be taking. I can mix the vegetables in with the main meal. The dried fruits (bananas to start), can be eaten dried or rehydrated.
My breakfast planning has never succeeded. Or rather, I never follow my plan. When I get up, I want to pack up and hit the trail. I hate breaking out the stove again and spending a half hour cooking and eating. I do drink water, so I'm hoping a breakfast protein shake will survive trail execution. I'll either use granola/mil or breakfast bars to provide some extra calories, and I can eat those at my camp sight or my first on-trail quick stop.
Snack planning is also something that never really succeeds. Most of the food I still have when I get to the next town are snacks. Except for the Clif bars, I actually like most of the snacks. But I don't like long stops, and you can only snack so fast. My brief stops are usually about 5 minutes with a lunch stop of up to 20 minutes. My planned dinners make me full, so I don't have the appetite to eat unused snacks.
Bottom line here is that I do the best planning I can. But the plan will not likely survive the trail.