Just saw the episode today. A good episode, IMHO, and better on the second viewing for me. I was expecting a few things in this episode that are still-to-come, so that was a minor disappointment. Carl Lumbly (Martian Manhunter) also struck me as very flat this episode; Batman ejects from the Javelin, sustains severe injuries, and he says, "Batman? Are you there?" as if he had no idea Batman's life was in danger (which he did, of course, since they were in radio contact). It also irked me a bit that Batman had to charge to the rescue there. Batman's one of my favorites on the team, but really, there were several other ways they could have handled it. The simplest would have been to beam down the Martian Manhunter himself to deflect the missile. Green Lantern probably could have handled it fairly easily also, and even if they couldn't beam him down, he should be faster than any Javelin (although, we didn't see him around when the missile had been launched). Those are, however, fairly minor things.
The second time through, I checked for consistency, and they were indeed consistent here. In the comics, Doomsday was linked to the Cadmus Project, but they mention no such link here, and it seems that he did, indeed, precede the Cadmus Project (on this show). The Luthor for president is stretching it IMHO, given his criminal record, but he's got the money to "spin" it, and if the two major parties had slim pickings, then it's certainly conceivable that Luthor could pull it off. Especially if he used his influence to manipulate things behind the scenes.
I did really like how they're showing certain government types being afraid of the League, and rightly so. Having Batman beginning to come around to their perspective, becoming afraid of the League's power, was also cool in that it mirrors the comics in a few major storylines. In Kingdom Come, Batman opposes the League and forms his own team of superhumans to oppose them. In Squadron Supreme (Marvel's JLA counterpart), a similar thing happens with Nighthawk (Batman's counterpart) forming a rebel band to keep the Squad in check. Then, of course, there are the protocols that Serge mentioned. As the only one without super-powers (inborn or artificial) in the League's core team, he's the logical choice to be most concerned about superhumans going rogue. I'm eager to see where they go with this.