I'm fine with the league set-up (though I'm probably one of the few people who think inter-league play is a must). My point is more about the composition of said leagues. It's not like the jays or expos existed in 1901, why not put them in the same division, or at the very least the same league?
This might seem ideal, but for that to happen teams would have had to move from division to division or from one league to another pretty frequently to accommodate what the MLB might try to shoehorn as a new rivalry as the league expanded in the '60s and '70s.
For example, the Washington Senators and the Angels came into the league in 1961, expanding the MLB team total from 16 to 18. They both became AL teams as MLB always kept the number of teams per league an even number up until year-round inter-league play so that there was never a team in each league idle at any given time. If there were 9 teams per league then, and they didn't play inter-league then 8 teams per league would face off against each other, leaving the 9th twiddling its collective thumbs.
They could've put the Angels in the NL to be a rival for the Dodgers, but then they'd lose out on a potential Washington/Baltimore rivalry. Or if they wanted to try and force both, they'd need to move a third team from one league to another to keep the team numbers in each league even.
The following season the Mets and the Astros came into the MLB. They could've put the Mets in the AL as another rival to the Yankees, but then they'd have to put the Astros in the AL as well, and the AL would've had 12 teams to the NL's 8, instead of 10 and 10. Or they could once again move teams from 1 league to another.
The MLB could've had to realistically rearrange divisions and leagues 6 times from 1961 to 1998 to try and manufacture rivalries with teams as they come into the league, breaking up established rivalries along the way. As steeped in tradition as baseball has been, that wouldn't fly. The addition of the DH in the AL in the early '70s would've further complicated matters if teams were forced to move back and forth to accommodate these newer rivalries.
Imagine if MLB had to rearrange its leagues/divisions and possibly break up the NYY/BOS rivalry or STL/CHC rivalry because they were forced to move 1 team to a different league to keep the teams per league an even number just so they can try to make a Miami/Tampa Bay rivalry. Would you have wanted that? I wouldn't.
Of course, if MLB really wanted to do this now, they could. They no longer require an even number of teams per league as year-round inter-league is (most likely) here to stay. MLB would make it a priority to not break up traditional rivalries in trying to create newer ones. Still, this would take a decent effort to re-align the divisions in a way that most find amenable and I don't really hear much clamoring for this.