This is a little absurd, but what if the series is a time paradox? Roger IS Luffy, Rayleigh is Zoro; so on and so forth. I know it's been done before, but rather than going forward in time, what if somehow, the Strawhats were thrown back in time and ended up realizing that they themselves were the Jolly Roger Pirates? Would partially explain the similarities between Roger and Luffy, and their lack of mention of the fate of the crew. Granted, explaining how Rayleigh and Zoro could exist in the same room without collapsing the universe if they were the same person is complicated, but… yeah, this is a little too much, even for Oda.
Barring that, I'll go with Mmmbug's theory of Luffy being aged significantly by Ivankov's hormone injection. Although Brook seemed to indicate that Roger had been around a while (25+ years before his death, making him at least in his mid 40's, if he started his career around Luffy's age), considering that Garp looked to be in his late 40's - Early 50's 22 years ago, it's possible that Roger had at least somewhat of an age jump; no more than 10 years, but no less than that. I'd like to think that like Coby and Luffy (same age), Roger and Garp were also the same relative age physically, if not chronologically.
Hmm... I've actually come up with a third idea. How does this sound? An Island that ages you. Yes... This is the Grand Line, remember? Anything can happen. And even though it was (semi-okay) filler, we've already had time distortion in One Piece in the form of mist; who's to say there isn't an island out there that causes one to physically age during their stay on it? A few days on said island to set the log pose could mean a few years of physical aging; the price you pay to get one step closer to Raftel, and a reason that many people give up their pursuit of One Piece; the cost of shortening one's life is just too much. It's possible that Roger (and thus, Luffy) elected to stay on said Island by himself so the Log Pose would set, and aged him significantly to the point where it caused him to grow ill. Thus, what killed Roger is the same thing that will kill Luffy: the ravages of time.