Each season does have different arcs, though. At least two, from what I can remember off the top of my head. For example, season 3 is split into two main arcs, the first one is when the Winx go on their journeys to earn their Enchantix while the threat of Valtor, while still there, isn't the focal point. Once they've earned their powers the second arc has to do with dealing with Valtor. Season 4 had the first story arc with Roxy, and the second one with the Earth Fairies' quest for vengeance. Season 5 similarly had the quest for Sirenix and then dealing with Tritannus in the second half. Season 6 had the search for Eldora in the first half and the quest to lock the Legendarium in the second. The first half of season 7 was about the Winx meeting the Fairy Animals, who play an important role in the second half.
Granted, my memory of seasons 1 and 2 is quite rusty, so I can't really remember if they followed this formula. But the last 3 seasons have divided the plot quite clearly down the middle, around episode 13-14.