Heroic abilities can be awarded at the GM's discretion, too, when characters do something, well, "heroic". In the published campaign I'm running, the PCs will encounter an important Macguffin four times. I plan on giving them an HA for each time after the first they deal with the Macguffin, and probably at the end of the campaign.
Another thing about the Skill Increases as well: they're not automatic. You get a chance to roll and see if you increase it every season if you assign it one of the points from the narrative checklist, or if you rolled a Crit (good or bad) for the skill during the session. You have to then roll over the existing Skill's value to see if you increase it (meaning odds are against you the higher the skill gets.)
A couple of my players noted the skill they considered their primary (Magic School skill or Healing, for example) haven't gone up since we started due to bad dice rolls.