Right but they showed the stones in one of the very first episodes BEFORE the skeletons. The Stones had significance before the skeletons did, they were not just an afterthought. By making the Skeletons Rose and Bernard would have devalued the significance of the Light and Dark symbolism which is being further played out in Jacob and MiB. Just having Rose and Bernard find the stones and hold them for whatever significance they found in them. Sorry, but if they just turned out to be two side players from the series I would have been greatly disappointed.
For the record I'm not saying I think it should have been Rose and Bernard, I use them as an example of someone the fans were guessing at. But as an aside I'm sure as heck waaaay more invested in those characters than I am with Crazy Allison Janney....
Remember back in Seasons 2 and 3 when the plot lines were going in a thousand different directions, new cast members were being added willy nilly and we got bunches of story arcs? It was insane. Then they finally announced that they were going to have a finite number of episodes and end it on a specific date. Once they decided that the episodes tightened up, plot lines disappeared and one major story arc began to be developed more strongly. That tells me that because they had no idea in the early days how long the show would go on for, they were trying to give themselves wiggle room. If the series went for 10 seasons they couldn't answer all the questions early, and they also couldn't keep people interested in one mystery for 10 years. So they introduced multiple mysteries.
They could have sent this story any way they wanted to at that turning point. When they started dabbling in time travel people started hypothesizing that the skeletons were Losties. ESPECIALLY since Jack said "40-50 years old." That's a lot closer to the 30 yrs back they time traveled than the 2,000* yrs ago Mother and Brother were placed there.
We're talking about 2 skeletons, a black stone and a white stone in a cave. That is so vague. The battle between good and evil is the most used story line ever. Black and white signifying good and evil is a given. If you gave 100 novelists this premise you would get 100 different stories from that. They purposely gave themselves something they could easily adapt to any ideas they would have down the line.
The black and white stones we saw before the skeletons were backgammon pieces (if I am following you on that). Again, Black and White are basic ideas: Symbology 101. Could have gone in a gazillion directions with that.
Finally, my tell tale clue that they didn't necessarily plan on going with the 2,000 yr old crazy mama story from the get go? Jack and the 40-50 yrs old assessment yet again. Why not have him say, "There's no way to tell" when asked how long they had been there if they already knew it would be two millennia. They wrote themselves into the corner the same way they did when they had dynamite on a ship older than dynamite.
Basically, all I'm saying is that I personally don't believe that they knew the end that we are seeing now was exactly as they envisioned it six yrs ago. If it is, and I don't know how they could prove it with out a sealed envelope dated in 2004 containing this script, then I feel they handled it awkwardly.
*I mentioned elsewhere that I was listening to Jorge Garcia's podcast. His script said specifically that 2,000 yrs had passed. Until TPTB say otherwise, I'm going with that.