With a Rune you can summon a creature or immortal. Because of this it stands to reason that Rune Spells are more powerful than the spells cast by the creatures/immortals that are themselves summoned with runes. This is generally true but not always.
Many of the more powerful character spells can do just as much damage as a rune spell. Inferno is an 8th level spell that does hundreds of health worth of damage to many enemies. The Tremor Rune Spell does a similar type of thing...although the #'s are not exact. Character spells can also bring creatures back to life from the dead and kill...just like Rune Spells.
The biggest differences are just how the two work and their limitations (or lack of). I'll list these below.
1) No random damage. Everything is a set amount.
2) No random enemies/allies hit. Its a set amount.
3) No Magic Save. You can't avoid any rune spell with a Magic Save. If a Rune Spell says it kills a creature, it kills a creature.
4) Sphere immunities, magic protection, and other character defenses will not stop a rune spell. The only way to defend against a rune spell is with a defense directly from another rune spell or relic. For example, the spell immunity creature ability will protect from any character spell but won't do any good vs a rune spell.
1) Random damage. There are rolls for damage/healing on all character spells.
2) Many spells are random for enemies targeted (like 1d4 or something).
3) Many spells allow you to have a saving throw to avoid a spell altogether or to lessen damage.
4) There are many defenses to avoid spells.
Another thing to point out is the differing uses of Rune Creatures and Character Spells that summon creatures.
When you play a Rune Creature it stays in combat until killed. But creatures can also be summoned by other characters. Its a big part of the game. However, these creatures remain in combat for only 1d4+1 rounds.