Actually as opposed to the above comments I'm very grateful to Germany. The idea to merge Whatsapp with Instagram and Facebook would be a huge hit to our privacy and frankly would ruin a great product. The Whatsapp founder was fighting against it for years, I'm glad there is a meaningful pushback. People are leaving and criticizing Facebook, while everyone's still on Whatsapp and the fact it just works, is simple and doesn't bombard users with data (and doesn't sell users data) keep it as a very respected messenger. Merging it with Facebook would ruin it.
I don't know the reasons behind keeping Whatsapp and Instagram "separate" from the main Facebook entity, but I have to think this would go away if Facebook just merged them altogether into the "Facebook experience". Whatsapp by Facebook, Instagram by Facebook. If they made it clear they were all essentially one service, I don't think the EU could stop them.
Sort of like how Google can use your YouTube and eMail and search history (and browsing history if you use Chrome or their DNS), because it's all one service with one account. Or at least, they can do that for now. You could still have a stand-alone Whatsapp (just as Google has about 20 separate IM apps, Duo, Hangouts, etc...), providing the same experience, just re-working the legal things behind the scenes.