Archivist Adaptation

Using the Archivist or Rune magic in game can be an interesting and surprising variation from the Wizard. It provides clearly different abilities and descriptions while still being close to the familiar mechanics.
The Runic charge mechanic does mean that enemies should ideally last more that a few rounds to get the most out of the change. If they are unlikely to last long enough you can start them out with a few charges, or give abilities that grant the creature Runic charges from other things than casting Scripts.

Adapting a monster with spellcasting or spell-like abilities to use Rune magic is very easy. Just replace the spells with appropriate Scripts and slap a few runes on the critter to make a runic variant. If the spellcasting is secondary to the creatures encounter role adding an ability that grants Runic charges when performing its primary role will help integrating the Rune magic and make for a more interesting encounter.
A more difficult approach is using the Runic charge system to generate and pay for other custom abilities, without ever casting Scripts at all. The abilities might require charges of a specific Design/School or give different effects. While more complicated to make it gives the monster play very differently depending on how it generates and spends charges, eventually allowing the players to learn tactics for countering and exploiting the abilities over multiple encounters.

The Mirage Cage is a dungeon in the shape of a Rune of Counterspell. Anyone who sleeps in the dungeon automatically counterspells the first spell cast on them the following day.

In rare cases Guardian Scrolls that stay in close contact with powerful grimoires for extended periods can awaken. These intelligent constructs often show great affinity for rune magic.

Monster Ability: Runeguard
When the creature’s SR negates a spell the creature receives a Runic Charge of the appropriate Design. Any charges gained over the creatures maximum are lost without effect.