Interesting thread. I adopted two Saints from the SPCA three years ago and we're still working with shyness and aggression issues. It didn't become a real problem until I brought them, separately, to a local, unofficial dog park. Nakita, older female, is now able to meet and sometimes run around with other dogs. But ONLY if they approach her properly - slowly and indirectly. She's shy around people - it takes her awhile to warm up - but she's just quiet about it, doesn't get aggressive.
Bear, 4yr old male, has only been able to tolerate meeting one small dog (the most submissive dog on the planet, I think). Regarding people, it REALLY irritates me when they charge right up and start banging Bear on the head, without asking, without checking. He's generally very good with people he knows, but with strangers he definitely looks to me for direction/to be in charge. When people don't check with me first - even when I tell them to (I even put my hand out to stop their advance) - he gets confused, and sometimes goes into an aggressive stance and/or barks. This usually scares the crap out of the person and they look at me accusingly, as if to say "you shouldn't bring him out if he's going to act like that." The sad part is he's a sweet boy who deserves to go on walks and to the park as much as anyone but because of this tendency, we don't go very often. Any thoughts/ideas are welcome, as always.
I think every dog has their individual needs/issues and we have to work them out as such. I agree that our big guys get a bad rap around this, regardless. It sounds like you're doing the right thing. More power to you!
BTW - Bear is terrified of the vacuum, my hair-dryer, etc. He's a real pansy!