Wow, great theory! it truly does make "absolute and perfect sense". Uhhh, except that…
a. the island is not lost or missing; it's at the end of the Grand Line, as everybody knows
b. "rio" meaning "river" doesn't mean anything yet, and if it did, it would more likely have a connection to "death", since rivers are much more associated with death than time in mythology
c. time travel is not a theme in One Piece, has not been alluded to, and would be the cheapest, lamest excuse for why nobody has reached the island that you could possibly think of
d. that quote from Roger simply means that there's a trail to follow, as Robin explained... you know, a trail... kinda like a river
e. even if Gold Roger saying he would follow them to their "END" did have something to do with a river, there's absolutely nothing connecting the "END" to the "first", the "first" to "upstream", or "upstream" to "back in time".
f. just saying that it makes absolute and perfect sense doesn't mean anything
The way you come up with theories seems to be to totally ignore what Oda has been setting up, come up with some ridiculous and unecessary (but techinically possible! [only since anything is possible in manga!]) explanation, and then find as many distant, loose connections in the story as possible, make some extreme leaps in logic, and then say that it's the most likely possibility.
Now I'm not saying there's anything wrong with that, but that seems to be how you do it. I haven't been here very long but I can't think of a single theory of yours that came true.
I still think Raftel is the ruins of the Ancient Kingdom, and that the reason nobody has gotten to it is much cooler than anything that's been suggested thus far, and not just some lame cop-out like time travel.
EDIT: Ace did explain the logic behind being "upstream" meaning furthest back in time.
A. Speculation. People say it's at the Grand Line but only Roger (in modern times) has been there.
B. Yes, life is like a river too. But by your idea, they'd have to die to reach Raftel. Are you saying that's why Roger allowed himself to be executed? That makes even less sense than time travel, because if he's dead, what good was it?
C. Not necessarily. See B. Really, having to die to reach Raftel would be the lamest thing.
D. Yes, but a river starts at the base, where it meets a lake or ocean. If Rio is the first poneglyph, then it's logical to assume they're going upstream.
E. See D.
F. Yes, I know it doesn't mean anything. But it does make sense.
You know, my original theory was a lot less complicated, and it had to do with Aqua Laguna. It stated that Aqua Laguna was at its peak every 22 years, and the tides affected the entire Grand Line. In relation to location, Water 7 is at the almost exact opposite spot that Raftel is on the globe. Therefore, When excessive high tide is reached in Water 7, excessive low tide is reached in Raftel. When the high tide is in effect around Raftel, the nastiest Seakings of the Grand Line nest over the island, the likes of which even Shanks and Whitebeard could not defeat. Roger sailed in there and conquered it while it was at low tide, and there was probably a seaking or two left, which Roger was the only man to defeat it.
But as far as we can tell, Roger went to Raftel alone. That means that something involving the D made Roger the only candidate to reach the island.
I'm not saying that they're gonna Travel back in time. What I'm saying is that the island is stuck in the past, and it's not existent in present time. Maybe once a few decades or once every 22 years it appears in the future, but only for a few hours, and only those with D in the name can set foot near the island or be killed.
Either way, it's more likely than Raftel being a sky island. Why? Because the White-White-sea was fairly tame. And I bet you compasses worked up there. So it would be a simple matter of sailing to Raftel.