Yes, subsequent seasons are often rated more highly than the previous seasons.

As for shows like Naruto or Bleach, where the whole show is rated rather than separate seasons, the specifics of the MAL scoring system come into play. For a score to count, the submitter must have watched either 5 episodes or (I think, its been a while so this number is probably a bit off) 1/5 of the show, whichever is smaller. This means that while someone could only watch 5 episodes of Bleach, drop it and have their rating count for all of Bleach, anyone who did the same thing to Gintama would only affect the first season of Gintama, not the rest. To rate the second season of Gintama poorly and have it count you must watch around 204 episodes (or lie).