If the court system was failing them so miserably, why didn't they try to have the legislature intervene and change the law?
I don't think they realized that the fix was in soon enough.
Actually, while I think this case does highlight some of the problems with the judicial system, it's very difficult to change any aspect of the system without breaking something else.
If judges are fair and impartial, there are good reasons to have related cases go before the same judge. It saves a lot of time on exposition, and it discourages people from trying to "hedge their bets" in a case by breaking it up into smaller sub-cases in the hopes that at least one will land with a favorable judge.
On the other hand, it is quite clear that in this particular case, the rule that requires all matters in this case to go before Judge Greer is causing very bad effects. However reasonable the rule may be 99% of the time, in this case its effects are very unreasonable.
The question, then, is what to do. What I would suggest, though I don't know how this would work in practice, would be to establish a legal standard by which bench-trial findings of fact could be challenged (allowing the same for jury trials would probably require a Constitutional amendment). To prevent the system from being flooded by appeals of every single case, there should be a high standard of proof required to overturn any finding of fact, e.g. proof beyond a reasonable doubt that the original court was just plain wrong.
Under current standards, it is basically forbidden for any court to say that any other court's interpretation of evidence is wrong. Even if new evidence emerges which shows the earlier finding was factually incorrect, the earlier finding may only be reversed if such reversal can be done without impugning the earlier one, i.e. it would allow the judge to maintain that the earlier decision was correct for the evidence that was given. Further, new evidence may only be offered if the evidence was unavailable at the time of the original trial.
To use a somewhat extreme example (one where, admittedly, courts might bend the rules a little) supposed John Q Public is accused of killing Jane Smith. At his trial, he maintains that Jane Smith is alive, and he has seen her, but she has evaded any efforts to bring her to trial.
If John Q. Public is convicted and appeals his conviction, and Jane Smith walks into the appeals courtroom, John Q. Public would have to prove not only that she is still alive, but also--given he'd known of her state at the original trial--that he had made every possible effort to locate her for the original trial. If the state can convince a judge that John Q. Public should have been able to produce Jane Smith but was unable to do so, all the appeals in the world would be useless. [In practice, as noted, I think the state would make an exception in this particular case, but there have been plenty of cases where the state has refused to acknowledge the existence of evidence which is 100% exculpatory because it did not deem such evidence to have been presented in timely fashion.]