I think it ends up balancing out in the end tbh. Most people will only watch the newer seasons of a long series like Gintama if they have both seen & enjoyed the rest meaning they are much more likely to rate the new season higher. It creates a rating inflation situation where only people who pretty much know they will like the show actually watch that season and those people are much more likely if not guaranteed to rate that season highly.
We would probably see later parts of Naruto, Bleach, & One Piece on there too if they were split into seasons. Most people who continue watching at that point still really enjoy the show for one reason or another and it filters out all the people who gave up on it & rated it poorly in earlier seasons.
Ideally there would be a better way on MAL to deal with this situation since both vote bombing and the rating inflation previously described makes the rating for any show with multiple seasons a wash.
The best way to evaluate a show with multiple seasons is by just looking at the rating for the first season IMO (since that one will include reviews/ratings from people who tried but didn't enjoy the show). This has its own problem though where if a show actually changes in quality in a later season it could deserve a better or worse ranking than the first season.