Rune
Once A Fool
Or better yet Jaracove, use the actual encounter building guidelines in the DMG. CR's can be deceptive and are not they way to build an encounter. Use the XP budgeting guidelines (with the multipliers) that are suggested in the rules.
Well, better is a pretty subjective term.

The encounter-building guidelines are effective at what they are designed to do, and that totally works for some people. But, even then, they still can't account for variables such as environment and tactical approaches, on either side, nor, to some degree, extreme luck. Even with the encounter-building guidelines, practice is still the most important tool.
CR, as you mentioned, is not an accurate measure of encounter difficulty. It is, instead, a rough measure of potential lethality, which is not the same thing.
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