Here are some examples using equivalent weapons of the 1H and 2H variety. Both have an overall 100 DPS, but the 1H has an attack speed of 1.4 and the 2H has an attack speed of 0.9.
Ray of Frost (20 AP, 215%)
1H: Uses 28 AP per second, does 153.57 damage per hit, total DPS of 215.
2H: Uses 18 AP per second, does 238.89 damage per hit, total DPS of 215.
Arcane Orb (35 AP, 175%)
1H: Uses 49 AP per second, does 125.00 damage per hit, total DPS of 175.
2H: Uses 32 AP per second, does 194.44 damage per hit, total DPS of 175.
The same DPS over smaller hits, sure, but it uses about 65% more AP per second. In this respect 1H weapons just drain your AP faster, which results in lower overall DPS. Cooldown skills are a little different in the respect that though they might activate faster using 1H weapons, they have the same reuse period and AP cost as their 2H equals.
Wave of Force (25 AP, 200%)
1H: Uses 25 AP per 15 seconds, does 142.86 damage per hit.
2H: Uses 25 AP per 15 seconds, does 222.22 damage per hit.
So as long as you can stomach the 65% longer activation time, you do that much more damage for the AP you use.
Solution: Normalize AP costs for skills WITHOUT cooldowns, but normalize damage for skills WITH cooldowns. Keep in mind, though, a perfect 100% normalization would result in an unbalance favoring faster weapons using +damage enchants, but a slightly skewed normalization would result in 1H weapons doing more DPS with no-cooldown skills balanced by a slightly higher AP usage per second, and 2H weapons doing larger bursts for skills with cooldowns, offset by the longer activation times.