Since I do not know how your other co-worker reacts, a first step might be to ask them if they have any problems with Bob's behaviour. To do this in a subtle way, you could start a conversation like:
Hey, I would like your opinion on something. I recently noticed that I find Bob's ways of conversation annoying, and I am planning on addressing this fact with him. Or do you think that would be an overreaction?
Make it so that the conversation is about the fact that you want to address Bob. No gossip about how annoying Bob is, focus on you and what you are planning to do. Your co-worker can probably give the best feedback, because he is also present during lunches with Bob.
Disclaimer: Do not expect that you can entirely change Bob's behaviour to fit your own wishes entirely. If you are going to confront Bob about this, be prepared to adapt your expectations as well. Be prepared to find a middle ground! If you are not, and just want Bob to not talk to you, there is no other way to achieve this than being blunt, and saying this directly to Bob. This will not be good for your relationship with him!
As you said, Bob doesn't take subtle hints. You tried, so the best way is to just start a direct conversation about it. You could either do this on occasion (e.g. when Bob tries to start another conversation using a pronoun game), but my first preference is always to just take the Bob aside. Make sure it is just the two of you. You don't want to confront Bob with a whole horde of disagreement. Maybe you can book a meeting room, or go for a lunch walk, so if Bob raises his voice in disagreement, it is not heard by everyone. From what I gather from your question, Bob raising his voice is almost a certainty, so be prepared to handle it. Then mention what you mentioned in your question, but bring it gently.
You're a good guy Bob, but I really want to discuss something with you. I would like you to hear me out, and think with me on how we can improve this situation. Thing is, I really don't mind lunching with you and (other co-worker goes here), but ... There are a few things about your behaviour at lunch time that bother me.
You could explain your opinion on the pronoun game, how you would really like Bob to either come straight to the point or say nothing at all, ask him if he ever noticed that he gets louder when talking, and especially when someone disagrees with him. Also explain to him that loud disagreement in a workspace is not really a professional behaviour, and that is makes you feel bad as well, you don't like being shouted at. And if it's (as Vylix mentioned) a case of you simply wanting to lunch in total silence, you might just say to Bob that you prefer to eat your lunches in silence. Be an example, do not sound accusatory and at all times be clear that this is as much a problem for you as it is for Bob. If Bob raises his voice because he disagrees with you, keep a gentle and calm tone yourself.
Be sure to ask Bob his opinion. Bob might offer an explanation for his behaviour. Maybe Bob is talking a lot, and trying a lot of different topics, just so he can find something that you both can talk about? Sounds to me Bob is trying very hard to be sociable, and your 'subtle' responses of mm, yeah, and uhuh might make him try even harder. Maybe you could initiate a conversation more often, so it starts with a topic that you like talking about with Bob? Maybe Bob has other problems, that make he has trouble processing social cues?
If Bob and you can come to some sort of agreement, then take the occasional approach when his behaviour is running out of hand at that moment. Make sure you are direct, gentle and most of all: Do not embarrass Bob! This means keeping the reminders between the two of you, so make sure that no co-workers that have no business knowing can hear you reminding Bob that his voice is to loud, or that he is talking to empty air again because you and other co-worker are not interested in the conversation. And always follow up in the last situation by steering the conversation to a topic that is interesting.