Shoutbox

It isn't going to be fixed. Why should Plus! alter itself to make it compatible with other addons and vice versa? It doesn't make sense. It is just like Messenger Descovery Live isn't completly compatible with Messenger Plus! Live. You are going to be waiting for a very long time.

As the OP stated he needs certain features however only listed a few which have alternative options.

Like Patife®, I too would like that MSG Plus! and MSN Shell worked fine together. But not because I need docking functions and  stuff, but simply because MSN Shell can add emoticons/avatars in batch. That's a essential feature for people - like me - who likes to download tons of gifs and install them on MSN quickly.

By the way, that would be a cool feature for future versions of MSG Plus! Or maybe a script could do that.

Who needs Shell just for that like can just forbid MSN Shell to boot with Windows and only use it when needed.