Personally, I don't mind the "separate worlds effect", as you call it. I find it a little odd in all the Trek series that the main casts end up as best friends.
I think it's just part of the basic Trek concept that the members of the command crew mainly interact with one another and form the family or adventuring group that we are following. So, I can't say that it bothers me on a show like TNG.
On the other hand, I don't mind that DS9 strayed from that by introducing more supporting characters with strong relationships to the main cast, and by introducing more conflict within the main cast. I don't think this necessarily implies, however, that the cohesiveness of the main cast has to be lost. Season 2 is probably the strongest season in this regard, not because everyone gets along and is best friends, but because everyone interacts in meaningful ways. They work together, they fight, they argue, they get to know one another. There's an organic quality to their interactions that other Trek casts don't have at all, but which DS9 loses in the later seasons to a large extent. Never entirely, but there is less of it.
To take an example, overall the basic trend of Kira becoming more trusting of Sisko as the Emissary and as her commanding officer is good, but there was no reason to abandon all meaningful disagreements between them. Another example would be the rivalry between Quark and Odo which produces so much great material in the earlier seasons but which largely disappears in the later seasons.
Voyager had one of the worst cases of this because the show kept claiming that the crew was like a family, but it didn't feel that way to me because all we saw was the nine main cast members with a little Naomi and Icheb thrown in. By the final season of that show it's almost impossible for me to imagine B'Elanna spending time with the staff working in engineering, let alone being close enough to them to consider them a family. DS9 wasn't great in this regard either, but at least the "family" message wasn't there to feel out of place.
Well, claiming the crew is a family while not showing it is definitely a mistake, but that's Voyager for you.
The only problem I have with this system is the segregation of the Ferengi episodes from the rest of the show, and the fact that the writers only used them for "comedy". It was like there was an entirely separate show taking place within DS9.
The Ferengi are the biggest culprit. It would have been better to devise a way for Quark to be more involved with the main cast and less isolated in his farcical Ferengi universe. Admittedly, this would have been difficult, due to the fact that Quark can't reasonably serve on a Starship or get involved in the war directly, while on the other hand it's hard to imagine the other characters caring about his business affairs.
It's possible that, if one were redoing DS9 from scratch, Quark would have worked better as a semi-regular like Garak, where he could show up when you needed him and occasionally have an episode focused on him, but fade into the background the rest of the time.