Nothing Black Beetle says can be taken seriously, so let's throw all of that out. The only time we get any real insight from him is when he loses it when Supernova stops him from taking Waveriders' body. He says that it won't matter what he messes up in the time line because he's going to change something big once he's able to secure a means to safely travel further back.
The hints we were given are little things I noticed. Day of Death had the most focus on him but curiously it more or less compared him to Rip through out the arc. It starts with BB shadowing Rip as he searches Vanishing Point asking who he really is. Rips' panel next to BB even got some wondering if it was Rip. I don't think so because Black Beetle is not as skilled at time travel as him. He had to leech power from T.O. Morrow to be able to do jumps until he got the red scarab and is still looking for more powerful ways to travel.
But I think there's something interesting about how BB comments on Rip hiding his identity so well and then Rip later admitting that neither of them knows anything about the other. It seems like an intentional detail but I'm not sure if it's just a red herring or to show the parallel to hint at something deeper. After finding Black Beetles' system tap at Vanishing Point Rip wonders who is intelligent enough to even set that up.
When Skeets scans Black Beetle he says "impossible" apparently stunned. For some reason Skeets won't tell Rip that he was able to get something from his scan of Black Beetle. Skeets expresses doubts about Rip following up on it and once he finds Jaime he asks for his impression of Black Beetle. Jaime basically says he's either the craziest guy ever or the smartest as he's able to keep you off your game by saying the wildest things. Skeets seems to ponder this. Black Beetle only appears to have two scarabs at present, but wouldn't he have three if he was Jaime? That would be the blue one (Jaimes') the black one Booster picked up in one million and the red one.
If he's an old character I have no idea who it could be that makes sense. Perhaps someone from the multiverse. He seems to have a connection to the Beetles and someone Booster would know in the Origins and Omens reveal. If it was a new character then he'd have to at least look like someone Booster knows for him to be that shocked when he's unmasked. I do not think it's Rip because: a.) he doesn't know how to time travel without stealing objects, b.) he tried to kill Rip, c.) Skeets scanned Black Beetle and although G/D made a joke about Skeets scanning Rip a couple issues ago Skeets has never shown that he knows who Rip really is. d.) doubt he'd really think Booster is a moron and try to kill "Daniel" before he had a kid if he was.
Well why doesn't Skeets tell him? Looking back (not count Giffin and DeMatteis run) Skeets has always been trusting of Rip and often told Booster they should listen to him. There's only one time where he didn't: When Booster wanted to save Ted. Right when the Beetles come to recruit Booster our Time Master tries desperately to make him see this isn't going to work. He even uses Skeets trashed body to claim the robot needs him more than the newcomers. Instead of agreeing Skeets tells Booster to save Ted. Later on he asks that Rip consider how Boosters' heart is in the right place and asks if there's nothing else they can do to save Boosters' friend. I think it's possible that if Skeets found something connected to Ted Kord it would make him hesitate on informing Rip or Booster. But also notice that he had to ask Jaime because even with his scan he isn't certain and likely didn't get all the information.
Maybe this isn't so much a clue as Jurgens didn't write it but in 52 I noticed that Mr. Mind had to use Daniel to get into the bunker claiming that his DNA was close enough to Boosters' to fool the sensors. While I really doubt Rips' tech would be fooled unless he wanted it to be (especially by DNA that was seperated from Boosters' for so many generations) I do think current tech could be. If true that means that someone related to either Booster or Ted could enter the Beetle Cave. Matthew Struges of Blue Beetle claims the villain is a new character and while he had Black Beetle claim to be Jaime he was never unmasked. The only theory I can come up with is that he really is a new character with a strong connection to the Blue Beetle legacy. Jurgens focused a lot of attention on the similiarities between Rip and him during Day of Death making him seem more like Rips' equal. Why?
When you get down to it why did he go for a ride with Ted in a time sphere? Why drop his scarab for Booster to pick up? My theory? (Which will likely be very wrong.) That Black Beetle is a legacy in a respect because the only ID I can think of that makes sense with the clues we're given is Teds' son. This would haunt Booster, give a reason for Jaime to battle him and give Rip an ironic match up. It would explain why Skeets didn't tell anyone but also why he wasn't sure: he only read part of the DNA structure. Yes, he didn't save Ted and taunted Jaime with the idea that Dead Ted was coming. But it could all be part of the plan...or maybe he grew up hating Ted. Jurgens says he'll reveal it and has something in mind for #50 but this is all I can come up with.