First of all, I'm not a huge Batman fan. As DC goes, he's probably my favorite, but I'm mainly a Marvel guy so anyway. I have read some of the earlier books but not many of the more modern ones. I haven't even read Miller's stuff. Just wanted to preface with that so you'd know where I'm coming from.
1. Making Ra's part of the origin, including the convolution of Watanabe turning out to not be Ra's.
Again I THINK ra's is a more modern character (as opposed to classical) and I don't know much about his comic incarnation except that he has the (is it called a lazarus pit?) thing that keeps him young. However I actually think that what you mention above works, for me anyway.
2. removing Bruce travelling the world and acquiring his skills from numerous masters. Not just in martial arts, but detection, escape artistry, slight of hand, what have you. Batman's supremacy, and why he stands next to Superman as being one of the most effective crimefighters is because of his multitude of skills, not just because he has "ninja" skills (I put this in quotes, because the martial arts skills he studies in the film are BS anyway). It's ridiculous to make it appear that Bruce is the best martial artist in the world. What Bruce is, is just about the best strategist in the world. And having him develop many skills instead of just one more effectively shows his obsession.
A lot of that would have been interesting. I don't know what you mean by the the BS remark (ninjutsu is one martial art I never had any interest in!) but I think that because Ra's played so big a part, that they had him be the only teacher so that they could build that father/son or older brother/younger brother relationship, the effectiveness of which I suppose depends on one's personal interprettation. I don't know how they handled that in the comics. I DO know that in the book Helltown (I don't know if it's canon), Richard Dragon is training the Question, and Bruce and Shiva show up, and the remark is made that Bruce is one of the top 4 martial artists in the world. I would have liked to see him develop more of the other skills you mention but I feel about that kind of like I feel about Spider-Man not using more of his science skills in the films: it would've been cool but didn't really take away from my enjoyment of the film for me.
3.That they use the cheesy, cliche' main guy goes for training and in a short time is superior to the guys who've been training for many more years than he has. Having Ra's tell Bruce that he was now chosen to lead his assault on Gotham is even more outlandish. Why GOTHAM? Why not London or Washington?
I think the thing about Gotham is that, within the context of the story, Gotham is supposed to be one of the BIG cities of the world, and apparently it is THE most corrupt. With Bruce being one of Gotham's 'favorite sons', with connections to all the most powerful people, he was already 'ideally placed' to carry out the plan, although in light of the end of the film, I guess that wasn't really a necessity after all.
4. For my money, Batman '89, without showing the origin presented a far more obsessed Bruce Wayne than BB.
Keaton did come off as WAY more obsessed (and had THE coolest suit of all the films IMO!). Looked like it was straight off of Neal Adams' drawing board! Batman has been portrayed differently through the years so what is 'definitive' Batman to you might differ from what it is to someone else. There are those who may even think that the campy '60s tv Batman is definitive! Some could say that definitive means how the character is most currently portrayed but I disagree. The current interpretation of Spider-Man sure isn't MY idea of 'definitive'! But I digress.
By comparison, Marko killing ben did essentially nothing to change Spidey's origin, wheras the above points and more that I didn't list made Batman's origin very different, IMO.
For me (being a Spidey fan) the change of Ben's killer DID change something of the meaning of the origin, maybe just because 'the burglar' was actually a very important character down thru the years to issue #200 of ASM. If you change that, he is no longer 'the Burglar', he is 'the partner'. It just lessens his role which is the problem I had with it. BUT considering all the other flaws with SM3, that was minor by comparison. As for BB, as I said, I'm not so big a fan that those differences mattered to me (considering I didn;'t even know about a lot of them anyway!) but thought that the basic origin (from the original 2-page Bob Kane story) ws basically intact and expanded. Could there be a better Batman? Absolutely! But I was very satisfied with BB and look forward to TDK!