Let's look at it this way......Indian Batting vs Pakistani Bowling
Kohli very recently faced a Rampaging Amir in Mirpur where the ball was swinging very similar to how Waqar & Wasim used to do. He had to see off Amir to then counter attack on the other end. In the 90s team there is no such thing as counter attacking the other end, there will be practically 4 ATG level bowlers bowling at him constantly - at their respective peaks of course and would make it really difficult for him to get them Away.
He has to face the 2 Ws (arguably THE BEST pace bowling duo of all times), A pace demon who literally bowls 95+ mph every freaking delivery and an LOI ATG spinner in Saqlain - The first one really to master the art of spin death bowling and then of course inventing the Doosra.
The 5th support bowler would be Azhar Mahmood or Razzaq (both of whom were quite pacy during the 90s) almost 140+ish so again the reprieve of the 5th bowler isn't there as well. Kohli and Dhoni are the only ones even CAPABLE of playing these kinds of bowlers. Rohit, Dhawan, Yuvraj and hacks like Raina would be really made to look damn funny to be honest.
Now let's come to the bowling of India.
This is the lineup that they Indian bowlers comprising of Ashwin, Bumrah, Nehra, Jadeja and Yuvraj / Raina would be bowling to.
Saeed Anwar (The guy was for a brief period in the 90s competing with Sachin for the LOI record of Desmon Haynes - Most ODI centuries)
Amir Sohail
Inzi (Keep in mind his spin and Pace Playing Ability)
Ijaz (A competent Middle Order Bat)
Saleem Malik (A very decent Bat in the 80s and 90s - go check his records on cricinfo)
Rashid / Moin
Wasim
Razzak / Azhar
.......................................................................................................................
Result wise it's not even a competition in test, 9/10 it would be the thumping of epic proportions and the 1 / 10 would be the draw scenario if Dhoni and Kohli got stuck in. In LOI there is no seeing off the bowler scenario as well for either of Kohli and Dhoni so they'd have to take chances against an attack that has 4 ATG LOI bowlers - If you guys think that Kohli and Dhoni are good enough to hit out against Wasim, Waqar, Shoiab and Saqlain then.........Good for you but I personally don't see them dominating us in any way. (This is all my opinion - please don't just simply start bashing me now)
However, the above results would only matter if they play 100% fairly, i.e. no fixing etc is done in any of the games. 90s was a very dark era for Pakistan cricket as far as fixing allegations goes.