Only player that was missed was Shaheen, and may be Babar, because he could have opened or batted at 3 pushing Hari/Rizwan one slot down. Hafeez has done reasonably well in SAF (& in T20Is), but his absence was well compensated by Rizwan - don't tell me that from No. 4 Hafeez would have out done 73/95 stats for 219 runs. And don't forget, Imam was MoS in SAF ..... The equation shouldn't be done this way - an under strength IND beat PAK's first choice team like minnows in same venue, and their full squad lost a home series from 2-0 up to this same AUS side 3 weeks back.
I gave an explanation long back for another thread, which can be brought here again. To everyone's surprise, I actually rate All Time PAK ODI XII at per with AUS & WIN - the reason being PAK's AT XII has some of the top outstanding individuals in history, who can match anyone, in any XI, in any generation. You can put players like Imran, Wasim, Zaheer, Javed, Waquar, Saq, Qadir, Razzak, Saeed, Inzi, Mazid, MoYo smoothly in any team and can justify that .... but obviously, AUS/WIN will dominate 2nd, 3rd XII and from 4th team, it's not even worth mentioning.
This current PAK generation is suffering exactly from opposite - there is no "outstanding" individual, no player in the class of "irreplaceable". Take out Indian top 4 - Kohli, Sharma & Bumrah, Kuldeep - they'll suffer a nose dive. This is because these 4 are stand out among many average to good players - it doesn't matter if they play Ishant or BK or Shami or Pandeya or Shankar or Jadeja or Chahal and there are many such; but those 4 are absolute stand out among 1.4 billions. This has negatives and positives as well.
Positive is, if your team/generation is composed of top talents, the squad quality is so high that missing few players, even ATGs hardly matters - consider this French Soccer team - take out Pogba, Varane & Mbappe ... they can bring Coman, Osmane Dembele, Rabiot, Langlet, Laporte. AUS won back to back WCs without losing a single game in like 23 in a row, after losing Warne, Gillespee & Lee a week before the start of 2 WCs; Imran won 1992 WC after losing WY & Saeed 2 weeks back ....
Negative side is what we are going through with current PAK team - you don't know who is your match winners, who are your best possible combination, who are your clutch players under pressure. A bunch of average players forming a team that can bash lower ranked teams but can't compete at top level, because players themselves individually are not that good. A full strength PAK team lost to BD in UAE without Shakib & Tamim - and trust me, it wasn't one off ... you can hardly expect to get a team 12/3 and that team missing their top 2 players, still manage to be out of the contest by 75th over. Advantage of such team is you are not dependent of anyone - any player can be replaced ... IND can't replace Kohli, Sharma or Bumrah; Poms can't replace Root or Buttler ... can you say that for Amir, Shadab, Hasan, Babar, Fakhar? NEGATIVE is, team will operate constantly at lower level, which we are experiencing now - any combination is just not good enough.
If Faheem was "rested" from game one, he would have been "another in the list", which should make a perfect executive summery of this thread.