We've gone through so many different diets with my kids. We initially eliminated gluten and dairy, and tried to be as "wholesome" as possible. We noticed a HUGE improvement with my oldest daughter once she got off gluten.
Then my oldest did a food sensitivity test, and we had to cut out a TON of stuff, but we noticed nothing, so we went back on them (always off gluten and dairy, though).
Then we tried Paleo with them and noticed nothing. And my oldest, who has always been thin, started looking ill because she got so thin. Plus 2 of my kids have social issues as part of their symptomology, and having them on a Paleo diet made them stand out even more from their friends, so we decided it wasn't for us.
Now, they're gluten & dairy free, and we give them very little processed food at home. Because they're older, there are so many school events, birthday parties, playdates, sporting events, etc., where food is around, so we just ensure they're GF & DF at these times.
Basically, our diet is clean, homemade food. We don't do a lot of corn (and when we do, it's organic so there's no GMO), soy, refined sugar, refined oils (canola, soy, safflower, etc.).... I do do potatoes (because I want them to not get too thin. I also forgot to mention they are always RAVENOUS. And on strict Paleo, they were SO hungry all the time. No matter how much fat I gave them, they were always starving. So the carbs help fill them up. We limit rice, not so much because of the sugar aspect, but because of the high levels of arsenic in rice.
Aside from the amazing improvement of my oldest once we got her off gluten, none of the diet changes seem to have made any impact on them. For me, diet was a huge game-changer, so I guess it varies by person. I am Paleo at this point, and they eat a lot of Paleo meals, but it's not exclusively Paleo for them. Sometimes they'll get rice and I'll get cauliflower rice. Or they'll get GF pasta and I'll have zucchini noodles. Sometimes they get the cauliflower rice and zucchini noodles right along with me. Rice is such a staple for people who are GF, but I don't like them to eat it every day. Potatoes are great for them, because not only do they actually fill them up, but they are cheap (and with 4 people with Lyme, we already spend so much money on treatment and food). They don't really like orange sweet potatoes, but they do like white ones.
Oh, and we do organic and grass-fed as much as possible for meat / eggs and veggies.
Sorry I rambled and I hope I wasn't confusing.