Porsche and VW have a shared history over many years- both have been dominated by two families and it looks like they are now in disagreement about the way forward. Not a good position to be in considering the present climate.
Porsche do not want direct competition from within the VW group. The big concern will be around the VW upmarket brands- in particular Lamborghini and to a lesser extent Bentley. I think the ones likely to suffer most are Audi.
Lamborghini will be pushed further upmarket ( the updated gallardo has already done this), to stay clear of 911 Turbo, GT3 territory.
Bentley won't be allowed to expand thier range to include a 4x4 ( not a bad thing) nor a sub 100k car.
Porsche can't be happy that Audi built the R8 nor will they be pleased about models like the RS5 or TTRS. On the flip side Audi will see this as a hinderence as they are trying to compete with Mercedes and BMW.
All this is going to lead to friction between both sides but if Porsche do manage to secure a 50% shareholding it will make is easier for them but ultimately with a shared history and culture I would expect both sides reaching an acceptable middle ground. They do however need to resolve this issue of essentially producing products competing with each other in the marketplace.