I have tried a couple of times to finish the quest with the sapling which the guy prays for but the tree just look like its blossoming only in the middle and looks kind of weird then I read that it is supposed to replace the old dead tree with a sapling but we can't see it because the old tree stays visible? Is that going to be done in some new patch? Sure could make Whiterun look purty.

It was fixed with the first patch. Are you sure you're up to date?

(Wonders when I last did the quest so that I tried it with the sapling...) I will... get back to you on that!