Like I said, it was too late for Holy. They had brought this possibility up in the game earlier, so it's not like it just came out of no where either. Holy isn't helping Meteor, it's just not strong enough to stop it. The only part about that I could see as being confusing is that Red says it's "having the opposite effect". You can clearly see tha Meteor is just pushing through Holy though, so I don't see why so many people are fixated on that.
After the lifestream comes out it destroys Meteor. You can see it hit it and chunks start to spread.
Midgar was destroyed, you can see this in the 200 years later part. Nature has returned! YAY FOR NATURE!
Humanity is fine. The only reason Humanity would be destroyed is if Holy had decided they were a threat and that isn't the case. It was just something Bugenhagan brought up as a possibility. In the ending you see Holy go right past humans(Cloud and co. chilling in the airship) and it does them no harm. Instead it heads right for meteor. Sadly, it is too late and it fails.
The reason it doesn't show what happened to everyone is because it isn't needed. They already wrapped up each character's arc in the scene where Cloud gives everyone the day off the night before the final battle. Everyone's personal story is estentially over heading into the fight with Sephiroth. What more do you need to know about their fates? That Barrett ended up settling down and raising Marlene? We already knew that. That Cloud is now at peace with his past? We already knew that. The big issue left is the fate of the planet and that's settled perfectly.
I think it has great closure. Life is the theme of the game and in the end life is what saves the day. I thought the 200 years later scene was great. The children laughing is enough shown of humanity. We already know how the characters will deal, just hearing that life went on and the world is a much nicer place is enough. And as I said before, the visuals are great. I love the shot where you can see the meteor from as far away as Cosmo Canyon and all the scenes where it's destroying Meteor with it's nuke like force are really cool looking. THe ending being remade with modern CGI would be so awesome.
I don't know what else to tell you. I always found it to be pretty clear. I don't really consider it subtle at all. Maybe if you watched it again after reading what I have said you'd see it differently?