Is there any reason to not rune skills? From their descriptions they simply add additional effects (fire, greater area of effect, adds teleport, etc) and don't suggest any sort of trade-off. They don't seem to lose any of their original impact, but I may not be noticing among the hack-and-slash action.
If you have a rune, it is always better to use it. Blizzard CMs have confirmed that there is no reason to choose not to rune a skill, it is merely an issue of what rune to use. Of course, you might still want to use a skill before you have unlocked any runes for it, since a non-runed skill can still be "better" that a different, runed skill.
This depends on what damage type you are doing and what the runes do vs what the spell does naturally.
For example. You have lots of gear that give additional damage to Lightning Damage. You are deciding on what rune to get for "Spell A". The base spell does Lightning Damage. None of the runes do Lightning Damage, but you really want the ability. Well, use no rune.
Another example. The base ability compliments your current build better than any of the runes. Use the base ability instead of the rune.
They are not always better. Just depends on your build and gear. However, they are most of the time better.