Not really. God's waiting room (which is not actually God's) only explains the flash sideways. What happened on the island over the 6 seasons, happened.
The island stuff is what interested me the most, however, I'm specifically talking about the final (double) episode, when I talk about my dissapointment. I would say that most of the final episode (especially the final ending), was based around "God's waiting room".
Yes, Jack and Locke fought eachother, which I found acceptable in a closing episode, however, the actual ending which was in the Church, was a cop-out and allowed the writers to explain pretty much everything away as mere fantasy - a place that didnt actually exist.
Either way, complaining about it won't help as the series is now finished. I just feel that the ending was a cop-out. Even what happened on the island was very low-key, given that they were building up to the final scene for an entire season(6). I would've expected something a lot more spectactular to happen when Desmond went into the cave.
Anyway, I'm rambling, so I'll stop.