Preheat the oven to 450° and line a large rimmed baking sheet with aluminum foil. Put the beets, carrots, 2 tablespoons red wine vinegar, 2 tablespoons olive oil, 1/2 teaspoon salt and a generous amount of pepper on the baking sheet and stir to coat. Bake, tossing once with tongs, until the vegetables are tender and lightly browned, 30 to 35 minutes. Remove from heat and let cool to the touch.

Meanwhile, in a medium bowl, whisk together the remaining 1 tablespoon of red wine vinegar, the lime juice, the sugar, and a pinch of salt. Add the onion slices and toss to coat. Allow to sit for 15 to 20 minutes, stirring once or twice, to soften and lightly pickle the onion. (Or cover and let sit in the fridge for up to 1 day.) 

Place the chopped dill, lemon zest, and garlic in a single mound on a cutting board and continue chopping until the garlic is minced and the ingredients are well combined. 

Turn oven down to 400°. Brush the bread slices on one side with a little olive oil and sprinkle with salt; arrange on two large baking sheets. Bake until crisp and golden, 8 to 10 minutes. Remove from oven and let cool slightly. 

Assemble crostini: Spread each piece with about 1 tablespoon of creme fraiche and top with a few pieces of beet and carrot, and some pickled onion slices. Sprinkle with the dill mixture and top with more black pepper; serve immediately.