Some things were perfectly set up though, like in the first or second episode of S1, Locke holds the light and dark stones which upon rewatching the show is obviously a nice nod to what happens in S6 with Jacob/Man in Black. You also had the skeleton in the caves when they first got there which leads me to believe that they had the basic idea of Jacob/Man in Black, light vs dark mapped out in S1 already, but along the path things changed. Desmond, who is probably my favorite character in the show felt like he would just be a guest, but due to popularity he came back and eventually became Jesus kinda. Some ideas felt crazy at first, like the idea of moving the whole island by pulling a giant lever, but some of those crazy weird things also worked for me.
To me the show got more and more rewarding towards the end because you got to see more and more of the island and the gang wasn't just sitting around the beach. For example the temple that shows up in S6. At first I thought "why didn't anyone stumble upon it sooner?" but in reality the group really didn't explore the island that much in the earlier seasons. They found certain landmarks like the black rock which they would return to, but not a lot outside that. I definitely don't think they planned on introducing time travel when they started in S1. And to return to the praise for Through the Looking Glass, I think they kinda shot themselves in the foot when they wrote in the rescue at the end of S3 already and figured "oh crap, we can't take the characters off the island, because the show is at the island", so they wrote the plot line of how the characters returned. Things like that felt a bit "made it up as they went along", but other things felt planned. I'd even argue the smoke monster was planned all along.