So in essence it was because some people didn't understand the "replacement affect" rule?
That's the gist of it.
But not just "some people". Some members of the CAG/RC.
I don't want to sound like mean or anything but C''mon it wasn't that difficult to understand. A commander dies/gets exiled instead "replacement affect". Not like it is rocket science or some of the more complex part of the game.
Then to take a quote from that "A side effect of that rule was that cards like
Grave Pact wouldn’t trigger if someone’s commander was destroyed.
This was played incorrectly by many players, so we’d been looking for a way for commanders to behave “more normally”
for many years."
First of all I would say it was played incorrectly mainly by new players to magic and new players to commander. Once the rule was explained and understood then it isn't played incorrectly anymore. It is a simple misunderstanding of a rule that is easily corrected. Understanding how the "stack" works is much harder to play correctly compared to "replacement affect".
2nd of all C'mon many years?? You mean to say they couldn't come up with a simple solution until now?? Was it really that complex to come up with a solution and to think there are magic the gathering judges on this panel who for some reason couldn't come up with a solution until now??
Oh wait there is this which explains why a solution came along just now, "Fortunately, the RC’s Toby Elliott and WotC’s Eli Shiffrin are really good at clear, clean rules and
working with Sheldon Menery (at the time with a foot in both worlds), they found a way to make “dies” triggers work correctly without any significant corner cases. "
Of course Sheldon who'd have thunk Sheldon continually digs his heels in because of the mindset "it is my creation and I am not going to change a dam thing" attitude.
And significant corner case is
Roon of the Hidden Realm.
Exile someones commander and they choose not to put it into the command zone after it is exiled. Roon player can use
stifle, dissallow, timestop, and anything else that has a way to
negate roon's ability. Now the other opponent's commander is stuck in
exile for the rest of the game.