Unlimited customization can also lead to unchecked game imbalance. Note; can.
Granted, there's already 'imbalance' in regards to powers and stuff I'm sure - since that's why things are always tweaked (or nerfed), and those who find exploits and things are the ones best to find those imbalances - if they report it, or when they're caught.
(And yes, there's already imbalance since people are PL'ing to 50 in a day; but it's what the devs are trying to fix already.)
And unless the person who made the temp power of a nuclear bomb only available after the end of a 5-part mission for lvl 50's only... Sure, your arc may get really popular with the lowbies who like the idea of going into a difficulty-5 boss mission and blowing the crap out of everything in their wake solo.. but that would be imbalanced. Not to mention pvp.
Do I feel limited when trying to make an arc? Sure. Frustrated at times when I can't find what I want? Sure. Bummed that I don't have more save space? Duh. But it pushes me to find a way around the limitations and come up with a new way of doing things.
Currently, I see this AE stuff as a beginning.. when the bugs and exploits are worked out, perhaps there will be a few programmers who will be dedicated to add to the stuff we can customize. Or perhaps add more options for the current stuff.
Stuff!
Also - in my opinion as an artist, I see limitations put on us all the time. It just means we have to stretch out of the box a bit more and work around them. Will it change our final project piece? Sure. But perhaps it will be better for it.