This is probably too general of advice, but I’d recommend that if you expect to regularly use your iPad Pro as a tablet, the 11-inch will likely be your best option. If, however, you expect to use it almost entirely with a Magic Keyboard attached, the 12.9-inch is a good bet. Both devices can work in both modes, but the 11-inch is a better tablet, and the 12.9-inch is a better laptop.
I really enjoyed this article, as it captures a lot of my feelings regarding using the iPad as your primary computer. As my personal laptop begins to age, I find myself using my work issued MacBook Pro for most of my “computer” tasks, and an iPad for nearly everything else. The iPad Pro + Magic Keyboard combo is a very versatile (albeit expensive) solution for almost anyone now. If you’re going to go that route, the biggest decision is how much you want to use it as a traditional tablet.