I think that Patchou has his reasons for removing the 'Hide the ad banner' feature. Microsoft do include ads for a reason, to help pay for the free service they provide. Regardless of whether Microsoft do or do not require more money is immaterial. So Patchou has decided to be kind to Microsoft and leave out the hide ad feature in the upcoming version. As previously mentioned, you can use StuffPlug 2.0 to hide the ads.
One of the goals of Plus has been to never touch the Messenger Protocol. I am not sure how including a file transfer manager might alter this goal. If you already have Plus, check out
File Transfer Plus which is excellent for file transfers over MSN. Its only flaw is that not everybody has it installed. So spread the word!
Patchou has suggested that more advanced users might not find the sounds that useful, but I think they will be great for everyone. Remember there are probably not that many uber-l33t people using Plus and it should cater for everyone.
There are still plenty of other features in Plus that are really useful. Remember, Patchou hasn't reported the full list of changes in 3.50 so there are still some surprises in store for us all