this comparison has always fascinated me and still leaves me without clear-cut answers. This needs to be debated more, but it seems that most people already have their thoughts made up on this matter
My arguments will be as impartial as possible in terms of contents, despite my avatar.

Maybe you will feel a bit of a scent of partiality in the way sentences are constructed and in the rethoric department because my goal is to be an advocate of Duncan's case.
If we compare
Hakeem's 93-94 season with
Duncan's 02-03 season, Hakeem's advantage comes down to usage%, the ability to sustain a higher volume of scoring x game. How do you reconcile this gap with the fact that most advanced stats slightly favour Duncan both in RS and PS?
-----------------
Regular season: If we change the system of reference to "100 possessions" (as dhsilv has done above me)
Hakeem is favoured by 2 points,0.6 blocks more,1 steal more,
while
Duncan has 1 more assist,4 more rebounds
(
yeah this might seem a bit trivial but the differences in this comparison are so elusive that we need to explore the reductionist approach too)
Accounting for everything,PER gives the advantage to TD ( Duncan 26.9 vs 25.3 Hakeem), WS/48 and BPM too.
On-off for Duncan in RS +14. A staggering +23 in the PS,
We don't know about Hakeem.
(Hakeem has a clear advantage if we take his 92-93 regular season but that advantage also disappears in the playoffs despite playing also half of TD's games)
----------------
Post Season.x 100 possessions: The situation doesn't change much.
Hakeem beats Duncan by 6 points x 100, 1 steal more, 1 block more
Duncan has 6 more rebounds x 100, 1 assist more,
PER, WS/48, BPM, Ortg, Drtg, give the advantage to Duncan here too
Hakeem's opponents had an average of 4.3 SRS in the playoffs
Duncan' opponents had an average of 4.2 SRS in the playoffs (let's give Duncan some handicap because of Dirk missing 3 games...but the spurs were ahead in the series before the injury)
This isn't helpful as much as I thought though and we're not accounting for teammates contribution. Were those rockets w/o HO better or worse than those Spurs w/o TD?
-------
I'm glad I'm not the only one. I found an interesting thread opened by the user
trex_8063 two years ago who questioned the magnitude of this perceived gap between TD and Hakeem, I don't know if he's still concordant with his thoughts though,It would be interesting to know if he changed his mind:
viewtopic.php?t=1403048
Why is peak Hakeem named along with MJ,LBJ,Shaq,Kareem in term of peak playing while Duncan is relegated in the next tier even if the differences seem negligible or just based on raw stats? (at least to me) I feel like something is missing