Despite the long list of dodgy ingredients in Ensure drinks, there are people with Crohn's who have achieved remission through a liquid diet consisting of Ensure. It is lactose and gluten-free, believe it or not, so it could be worse.
That said, it's not a bad idea to make your own, healthier, versions of commercial drinks. But it's better to drink the commercial crap and get the extra calories/nutrients (as needed) than eschew them entirely, unless you do plan on making your own milkshakes and smoothies. I have no personal recommendations, as I drank Fortisips rather than Ensure - Fortisip is like the European version of Ensure. But their website has all the different versions and flavours.
/ensure.com/nutrition-productsI used to make calorific smoothies consisting of whole milk, peanut butter, and bananas. I'd make it unhealthier but tastier by adding banana nesquick, banana ice-cream and/or nutella to the mix - if I'm gonna drink a milkshake, then I want it to be sweet. It was proper nice, and if I needed to put on weight, I'd make them again. I also sometimes made savoury soups but it's hard to pack a lot of calories into a smooth soup - you can add double cream and that's about
it.
Edit: Is it the lactose or protein in milk which affects him, do you know? There are lactose-free versions of cow's milk you can buy, but that won't help if he's intolerant to milk proteins rather than milk sugars. Only alternative there is to use a non-dairy milk, like almond milk, coconut milk, etc.