I agree. Most of the time, DAs do not want to combine cases from what I have seen unless it's all the same episode, such as the Loud Music case, where the perp, MD, shot at a van with 4 young men it it and killed one of them. Instead of trying him for each count, against each of the men, the DA took it as an all in one. The case is being retried, as of now, by the way, a portion of it anyways.
It can get too confusing to try to mix both cases in one trial, especially when they are separated in time. Just like this forum did not like mixing the MH case with Hannah Grahams at first because it really did confuse things. Also, if there is a jury that just doesn't work, or the DA did not present the case in a way to get optimal result, the other cases are still available to put the perp away. Usually the strongest case is tried first and if the sentence is such that it would be redundant to try other cases, it often isn't done for financial reasons. IMO, the MH case will be tried regardless, given the parents' involvement in the case. I can't see the Harringtons letting it go, unless JM gets the chair. Even with guaranteed life, they would likely want their daughter's case be tried and justice done for her. That is often an issue with perps have multiple cases.
I don't know how much of "slam dunk" the 2005 rape case would be. So much time has passed. I believe the victim is out of country and it is possible she will not come to testify, and if she does, how much impact would her testimony have? The DNA evidence is what would convict JM if there is a direct match, but I believe the victim would still have to be here for the trial, or is that not the case?
I think the DA gets to choose how to go within constrains of state law.