Let's start with this one: you said, "The issue is, it seems like its not an app problem but a business deal or something. I don't know, but do you remember Joe Belfiore saying that the app is a problem,with GDR 3 and that 8.1 uses a different notification,core..."
We all know that WhatsApp has had notification problems on WP since... well, ever. We also know that WhatsApp is still using the volume hack even as recently as its most current version. You state you recall Joe Belfiore saying that it was a known problem with GDR3 and that WP 8.1 uses a totally different notification core.
So... if WhatsApp is known to use a hack and had known problems with notifications in GDR3, given that WP 8.1 uses a different notification core, isn't the logical jump that there must be really big, systemic issues with WhatsApp on WP 8.1 - as both WhatsApp and Microsoft confirmed when then pulled the app - and not some shady business deal that is certain to anger loyal Windows Phone WhatsApp users? No, that is an assertion supported by nothing since Whatsapp works fine for all intents and purposes on 8.1. If it was such a risk, Microsoft could have wiped it from everyone's phone
Isn't, then, the next logical jump that really big, systemic issues would require significant work and modifications to the application, larger than a quick fix, which might take some time to properly implement and test? Couldn't also an illogical jump be that maybe WhatsApp wants to take this opportunity to finally correct the hack they've been using [a hack, which is no longer in use you might have noticed.], which would require an entire new routine to be coded and tested otherwise there wouldn't have been a hack used in the first place?Apps are not physical goods. They do not need to be removed to be fixed. What ever world shattering problem it is could have been fixed without the app being pulled.
All of the logical evidence points to really big, systemic issues with the app. No one knows what is actually happening behind the scenes with any app they put on their phone except for that app's developers. No one sees the source code, no one knows what tricks, shortcuts, or hacks were used in writing that application, but we DO know that WhatsApp did use known hacks. How do you logically jump from "wow, this app is messed up, because it's messed up they don't want anyone else using it, and they're trying to fix it" to a shady business deal that seems to purposely eff with loyal users?