So apart from personal opinion (my theory is better than yours), what would be a good indicator that any given theory does indeed explain certain evidence the best way?
You have to honestly compare which theory says the most about the most observations and which theory’s shortcomings represent the least serious conflict with the facts.
For instance, let’s say that I want to believe that the creation of all life was a one-time event that occurred in a relatively short span of time 6,000 years ago, which is about 1,000 years before recorded history began.
That explanation beggars belief, from a strictly natural point of view. It would require that (for instance) the rate of radioactive decay in many different articles be very different from each other,. It would require that the weathering of rocks occur at different rates in different places. I suppose nothing is impossible, but that one ranks so far into the realm of the improbable that it would have to be miraculous. So, while someone might say, “Well, I think there is no other conclusion but that the miraculous must have happened,” I cannot see how they can possibly berate anyone for proposing alternative scientific theories that do not involve miracles. The grace to believe in miracles should not be required to accept a scientific theory.
Science, for its part, sometimes has to admit, “in light of the evidence, we don’t have a theory based on natural law that is at all plausible.” That is as close as science is going to get to “maybe it was a miracle,” because the miraculous, being above being put to test, is by definition above science. Science can only say, “in our current state of understanding, we have no explanation for this that is even plausible.”
I think evolution meets the criteria of being plausible as far as it goes. It has problems; it might not hold up in its present form. There might be, for instance, discovery of a mechanism for macro-evolution (that is, the appearance of new species with chromosomal arrangements incompatible with any previous species) which does not occur due to random mutation. The mechanism for that might be very different than the mechanism by which some forms of the same gene come to vary within a single population.
I have yet to see an explanation for simultaneous creation of all life 6,000 years ago that can explain the fossil and anthropological record as simply weathered artifacts originating in that era. That kind of thing can conceivably be true, but such an explanation is not within the realm of science. It would be a miracle, and science is not in the business of declaring miracles. Science can only declare the absence of a natural explanation for a body of facts. It cannot declare miracles.