The phases aren't intended to be hard rules, but rather guidelines that could be ignored or adhered to as the GM desires. Each phase could assume that the GM distributes a certain number of skill points in each phase. Virtue points would be rewards for major quests or challenges.
The phases could also be used as a baseline for measuring monster difficulty. The current range of monsters is;
>Minimal Threat: Tiny enemies, mooks, or minions that pose no serious danger by themselves. Often come in groups. (Keese, Rope, Miniblins, Octorok, Zol, Stalkin/Stalchild, Deku Baba)
>Low threat: More capable than minimal threat monsters. Slightly more health and begin to show unusual defenses. (Bokoblin, Peahat, Armos Statue, ChuChu, Hylian soldier, Bari, jumping Stalfos)
>Moderate threat: The largest category. Monsters begin to have more elaborate defenses and weaknesses. Dangerous "duelist" type monsters start to show up here. Often make good minibosses for beggining characters. (Stalfos knight, Lizalfos, Moblin, Dodongo, ReDead)
>High threat: Dole out and take even more damage than usual. May have more than 3 actions. (Mothula, Darknut, Iron Knuckle, Hinox, Gibdo, giant Stalfos, Wizrobe)
>Extreme threat: Highly powerful monsters, usually powered-up versions of other monsters. Rarely fought outside of miniboss battles, but not quite tricky enough to be bosses themselves (Mighty Darknut, Grand Wizrobe, Stalmaster, Magmanos, Dead Hand).
The skill level scaling of the PC's would generally follow the stats of the monsters. High and Extreme threat monsters would still be highly challenging and dangerous for endgame characters, but average threat monsters would become minor obstacles at that stage.