Across The Sea should have been the first episode of Season 6

The episode is forever controversial because of its placement at the end of the series and the fact that it's a major mythology download right at the very end which makes it feel shoehorned in and doesn't really flow with the show naturally.

If they had actually placed the episode as the premiere, it sets the tone for the entire season, sets the stakes, gives real credibility to whether MIB is actually in the right throughout the season and allows the rest of the season to flow much more naturally.

That said -- I understand from a 'television is a commercial enterprise designed to make money' standpoint why they couldn't do that, especially after the Season 5 cliffhanger. Maybe you can get away with that on a streamer or cable. Definitely not network TV during the era Lost aired.