Aside from added feats, spells, etc., Pannotia makes use of a number of changes to the core D&D 3.5 edition rules as well as new homebrew rules.
Many of the new rules can be summarized by the following statement: characters and creatures in Pannotia are stronger than you might expect.
Rather than gaining +1 to an attribute at levels 4, 8, 12, 16, etc., creatures gain +1 to a single ability score at levels 2, 6, 10, 14, and so on. At levels 4, 8, 12, 16, etc., the creature or character gains +1 to all six ability scores.
Note: Creatures with special limitations on an ability or a nonability, such as animals (Intelligence < 3) and undead (no Constitution score) retain these limitations.
Instead of cross-class skills costing two skill points per rank, they will have the same cost as class skills, at one skill point per rank. However, the maximum number of ranks in a cross-class skill will be the same as normal, or one-half the maximum number of ranks in a class skill.
All of the monsters in the SRD have been reverse engineered and rebuilt from the ground up using the updated character creation rules.