Great discussion. I've done my own thinking about this over the years, as well.
Another reason why Bitcoin would make much more sense as collateral is that many people trust and understand bitcoin so they know they can force settle at any time and get their bitcoin back.
That's exactly right, IMO. Bitcoin has always been the crypto to rule them all. But the point of Bitshares is to reward BTS holders, so BTS loses its investment potential if you sidechain BTC into it to use as a backing asset. In fact, I don't know why you wouldn't just drop BTS entirely and run the entire chain as a bitcoin sidechain, with BTC instead of BTS as the core token.
And this is (one reason) why it hasn't happened. It leaves BTS holders with nothing. But sidechains also have security challenges of their own.
That said, I actually think that BTS makes for very good backing collateral, and the criticism from R3 can't really be fixed "inside the system" at all, so to speak. It will just gradually diminish as the market and stability for BTS grows.