Imagine if someone lost a tennis match 6-5, 0-6, 6-5 and claimed they should be considered to have won "because they got more total games" (16-12). That wouldn't be legitimate, because the agreement they played under was you'd win based on sets, not games.
Imagine someone won three blowouts, but lost 4 close games in an NBA finals. Them claiming they "deserved" to win because they got more points would not be valid.
This is what people who complain about winning the popular vote are doing; there was already an agreement about how a winner would be determined, and you can't change it later.
Same thing for baseball - "I should get into the playoffs because I got more total runs this year" is not legit. It's a type of renegging.
Attempting to change the system is perfectly okay, though. Just not claiming that you "actually won"
Lots of sports have "electoral-vote" type systems already in place.
Both methods are used and valid in certain contexts. Wiping the slate clean makes basketball series way more interesting - it would be terrible if ever series went 7 games and one team was effectively ahead by an 50 points to start the last game.