The thing is, if it was indeed Burke, how did law enforcement decide it was "first degree murder"? I mean, maybe they were just covering their bases, but it seems like even if they suspected he did it, it would be hard to say it was premeditated. If they had evidence of a long term plan from somebody, it seems like that would have come out at this point, and charges would have been pursued. Even if there were a few minutes or hours of premeditation, with a young child, I'd think it would be considered second degree - a kid losing control. That would make it a lot easier to get a conviction, given the circumstances.
Prosecutors decline to press charges that are presented to them by cops or even grand juries regularly - I know there were questionable actions by law enforcement in this case, but it's not an outrage that charges weren't brought after an indictment. There can be enough evidence to charge but not enough to convict. That's why there is discretion. It's entirely possible they just couldn't figure out who did what. This whole thing is so weird - so we know for sure the grand jury had a lot of info we don't have? It seems like it somehow would have come out by now. This case is so weird.
ETA: I know a lot of people think the Ramseys would turn on each other if it wasn't Burke they were trying to protect, but that's just not necessarily true. There are plenty of cases of people covering for someone who was not a child - fear of being alone, or of what will happen, or of the press, or losing financial support, or just being under the spell of the parent/spouse/whoever. Most people wouldn't stick with a spouse who did that, but plenty of women stay with predatory men, and plenty of men can't stand up to crazy women. It's not shocking to me. There would have to be a lot of complicated dynamics leading up to it, obviously.