Basically every 3 or 5 levels or so, starting at level 15, you gain an elective skill or rune choice. This way people will have a good understanding of how to play by having a structured start, while keeping imba skills/runes out of lower levels of game play. This way most thematic builds should be complete or nearly so by the time normal difficulty is finished.
Those wishing for variety will have it, at least until endgame where realistically all competitive players will be identical no matter what system is in place. Those wishing for choices to matter will be able to make conscious decisions regarding the development of their character. Those who would make bad choices in a free skill point system are not punished nearly so hard as they will have a viable base of skills to start with that will grow progressively regardless of their choices.