Put the soaked, drained beans in a 5- to 8-quart slow cooker, and season them generously with salt and pepper. Add the reserved Parmesan rinds and the wheat berries.
Warm the oil in a large skillet over medium-high heat. Add the onion, season generously with salt, and cook, stirring occasionally, until softened, about 5 minutes. Add the fennel. Continue to cook, stirring often, until the fennel is softened, and the onion is lightly browned, about 5 more minutes. Add the celery and garlic, and cook, stirring, until just softened, about 1 minute. Add the fennel seeds and red-pepper flakes and cook for 30 seconds more.
Add the wine and cook, scraping up any browned bits, until almost evaporated, about 2 minutes. Add to the slow cooker.
Add the rosemary sprigs to the slow cooker. Cover and cook on low for 8-10 hours, or on high for 4-5 hours, or until the beans and wheat berries are tender.
Remove the rosemary sprigs. Stir in the parsley and lemon juice. Season with salt and pepper to taste. Serve topped with grated Parmesan and reserved fennel fronds.