Vger has been dealt with in the comics and is not an issue moving forwards.
I hadn't realized it was addressed in comics. I'm not sure how canon that is but if it is, that's certainly an interesting take on the whole Vger plot.
In any case, I strongly feel that the Klingon War will be a huge part of the next film. They will probably play off of that whole "Klingons have it out for Kirk" plot line that we saw so heavily in ST3 - ST6. Only this time they will probably just blame him for the squad of dead warriors that Kahn killed. Or, as I mentioned earlier, the Klingons will try and take Kahn and his people to create their own augments.
Or...they could do the brave thing and go in a completely unexpected and original direction.