Yes. There's a somewhat clear divide between the seasons, which is rather noticable on a rewatch, but probably not so much when you watch the show on a weekly basis for six years with a lot time passing between seasons. Like anyone needs a spoiler warning for an almost 20 year old show, but, warning. Spoilered more to keep the post short than to hide the spoilers.
Uh. In the face of this Sailor Moon'eqsue plot, people's problem with the ending was that the characters meet in a church, with Jack's father, who is aptly named Christian Shephard, ushering them into the afterlife after Desmond makes them realize what is important and how to let go.