you are missing the point.It is not how the characters appear or act later, you get most of the clues when they FIRST appear and interact with Conan the first case their in.
Started out looking bad (touch Sokono) but was actually helping her and stood her ground in her fight with Ran.(chapter 768 page 4) At the end of the chapter we get a hint about her. And the next chapter tell us more about her.At the end of the case, she is pictured as a class mate of Ran. Note she is given a lot of lines and it is clear she is very smart But most BO member look a little evil and do in no way look nice. It is clear from this first case she is good.
Tequila -evil looking, Six lines. Nasty personality and of course a one shot. Very different from the nice good ones (Chapter 114 page 12)
Sabura - Haibara feel the pressure and you think one of the three must be BO but then it leaves, That should mean since the three are still there, that NONE of those three are BO. The BO is in the background and unseen. That is our first hint about him (Chapter 622 Page 12) . He is finally talking to the Police (Chapter 623 Page 7). He sounds like what he claims. He is a student at an university. And he is kinda drawn neutral, not really looking evil or good, kinda of in between. Him talking about his color also shows neutral. But He is not cold hearted. After all, he watered the flowers, and he feel better when he see green like trees in the mountains. I get the feeling he is a loner and like things to be quiet. These hints goes even more towards him not being bad. When he starts talking about Holmes ( Chapter 623 Page 13 ), he is smiling. That might suggest he is on the side of good as he would be more on the villains side if he were bad. More evidence comes up by how he learns about Asaga. Note he is quiet until he hears the word " Professor". If he was a BO guy want to spy on Haibara, he should have been more forward about getting a place near there. Also think like this. He should know where Kogorou Office is, as he is famous, so if he was bad, why is he staying there? Why not stay much nearer to either of his targets. I am sure the BO could make it very easy to setup where they want using heavy handed tricks if need be. That by it self is more proof that he is not BO. And since he is a student, it makes sense for him to be interested in helping one. By doing that, he gets a tutor of sorts.
Jodie (Chapter 270 Page 5). The first thing we learn watching her (not the comment before that) Is that she is good with a gun. But there is another a key clue there as well. She does not mind being in the spot light. Most of the people like that or maybe all turn out to be good. The look on her face while she is shooting is not an evil glee, it is more of a this is fun. I do not think the BO would be this open about how good they are at shooting. So another suggestion about her not being BO. More clue about her being good. She does have a good reason for wanting her day activity keep secret. And she is very out going. She gets quite a lot of lines and is very friendly. So far we got a whole lot of signs of her being good. Next chapter she how she reacts to the police, she is not hiding at all. Again she is even very out going with them. More evidence of being good. Also as part of the last chapter we also learn she is good at driving. At this point (Chapter 271 Page 15) we get a glimpse of her true character. She like Conan knows a lot. Suggesting she might be a detective. We get yet another major hint towards the end when Jodie talk to Sonoko about "A Female American Police Woman" which of course as we learn later is exactly what Jodie is.(Chapter 272 Page 17)
Araide (Chapter 234 Page 7) Again we got a person who does not look evil, has a out going personality and is nice. He is friendly and Kind. Later in the case he can see he cares about others like the way the helped the maid with her hurt arm. He looks like he might be a bad guy as he in a way at time fighting the police, but still he was straight with them and not hiding. And then we got Ran. Her reaction to him is interesting. She goes through all that just for a sweater for Shinichi.And when you add his grateful comments at the end, it becomes clear he is on the side of good.
Two for the price of one First the one shot Pisco. Old looking, a little like James Black and grated on the surface look maybe even nice, but these are still clues of his true character (Chapter 240 page 5). First at the start with the police he got only two lines. Later there is no question about him being a bad guy as he and Gin have a talk.
Next Vermouth (Page 240 Page 4) She has a bout her an evil beauty. She has only one line and that is through an interpreter. At the end of the case there is no question as she is in the car with Gin, We also learn she is a actress and just flew in. Clearly Bad
Still looking for the first Akai appears