This is a suggestion with multiple points to it.
1: Daily limit feature for magical items. I know the implementation of this will be difficult, however, it would be very helpful. I think adding a drop-down list under Spell Type on the Choose Spell Dialog for Command Word custom items would be able to do this. The formula for daily use is pretty straight forward, multiply the total by "daily uses"/5. This makes 5/Day items normal cost and 6+/Day items more expensive, while less than 5 days cheaper.
2: Adding Custom Magic Item spells to the "Magic Item Spell-like Abilities" section of Character sheets. This is automatically done for standard items, but not custom ones.
3: Calculate material costs into custom magic items. This one requires going back to all the spells and adding a value for the material component cost. This cost is already seen in the scroll/wand cost for spells, but when adding a custom magic item the cost of the material component is not added.
4: Removing non-standard cost increase for custom magic items. This is something I could not find a rule for in creating custom magical items. I could be wrong, but it appears that in Pathfinder a +2 Con Crown is the same as a +2 Con belt. 3.5 had a "Non-standard slot increase" which was 1.5, but PCGen seems to be doubling the cost for custom stat items in non-traditional slots.