Here is how:
1) In a limited conventional scenario the FGFA or any planned IAF induction cannot impact the PAF sufficiently for the PAF to be unable to do its job. This would only happen if the PAF were reduced to the point of being incapable of carrying out its operations, and that situation would not be consistent with a limited conventional scenario. You would basically be talking about FGFA/IAF aircraft destroying the PAF in the sky or on the ground... this, under no definition of the term, would be a "limited" scenario. Therefore, in case 1, the FGFA does not lead to a different outcome of the Indo-Pak engagement.
2) In a total war scenario, much before the PAF is eliminated the nuclear threshold would have been crossed. In that case, to more directly answer your question, yes, Pakistan's first use policy would come into play and the Sub-continent would be reduced to ash. FGFA or Mig-21, they would all end up as the same radioactive lumps of disfigured metal.
3) In a very limited Kargil or Siachen like scenario, air power will have such a limited role that the capabilities of the FGFA will not really come into play. So no real value here either.
Thank god at last i got an answer...Thank you Tech Lahore Sir...Otherwise all i was hearing was fanboy statements...If you don't mind i have some counter questions....
1) Sir i cannot vouch for how good/bad FGFA would be because the specs are not yet out...However ruskies do come up with good planes...
All i know is that kill ratio of F22 vs MKI would be 99:1 if stealth is there....bcoz F22 would be firing its missile at the time when MKI would not have any clue that
combat is ON.... Now with FGFA in picture i just don't get what counter measures would be taken to stop FGFA from entering Pak Air Space and pounding sensitive targets... Also how successful can be any PAF operations inside Indian Air Space??? Mind it i am not saying 5 generation planes are invisible but because of stealth and no true counter measure against them win probablity tilt towards them by a huge margin....
In short would it be true to say - where ever you would face FGFA there is a high probabilty that you will loose that particular battle...unless and until you have a good enough countermeasure??... All i am asking is what are those countermeasures...
P.S : I am insisting on this question because i strongly believe that there is no way PAF can let IAF increase parity between two forces that there is no point of return...
I honestly don't buy the argument that Nukes would be an answer to everything...
Here is my opinion - The only possible counter measure at that time is speedy induction of China's 5 generation Plane... PAF would have to wait till China come up with an alternate and hope it is good enough to challenge FGFA...Secondly economy needs to be good to back such inductions... FGFA is going to cost $100 million per Plane so inducting 5 generation plane is not easy....
2) I totally agree sir... Even if you look at controvertial doctorine of Indian Strategist aka Cold Start it gives an impression that every one is way clear that whatever be the strategy nuclear threshold should not cross... So i am of strong opinion that unless and until some rogue general take over this situation will not arise...
3) I do not agree with the third point of yours sir...Kargil was an eye opener and we all know how Israel helped change the results to India's favor...LGB had limited role to play but i am more than convinced that in future war of that kind Air Power will play a much bigger role than what they did in Kargil...However i must say FGFA would not be of any use since you don't need stealth to take on enemy without any Air Cover...
The only scenario in which you can build a strong case for the FGFA having a bearing on the war in a material way would be an extended conventional conflict in which both sides never cross the nuclear threshold. However, given the doctrines in place, this will not happen. Pakistan has developed its nuclear weapons to destroy its enemies if it is threatened seriously. Not to sit idly by in case the outcome of a large scale future war is going against it.
I am not in agreement with this as well Sir...If nuclear threshold is not crossed then why would a country use nukes to destroy her enemy and kill helself as well??? if there is no serious threat on the existence of Pakistan then i doubt there would be any use of nukes unless and until some rogue general thinks that his/her ego is more important than millions of human life..
Till then the brilliant brains behind PAF would already be thinking about ways how to deal with this "out of the world invention".
And I believe they can deal with it because they have a huge experience of capturing IAF aircrafts, destroying IAF aircrafts and bombing IAF airbases. 
