My personal opinion on character customization is that the fun comes in when you can actually understand the rules:
If I hadn't played AD&D at the time when BG & Co came out, the character development wouldn't have had half the appeal to me, personally.
Now to the question / problem I am seeing: With an IP game like PE, where the rules are developed by Obsidian themselves, the problem could be that those rules are too hidden from the player. There are two sides, of course: On the one hand you want to have it as complicated as possible, to allow many options and leave as much room for customization. On the other hand: How do you present to the player in a concise way, how it works? And also too much information could frighten some players.
What I would like to see is a complicated system with the option to be swamped with information. E.g. like in the old IE games where you could print out every dice throw in the dialogue box. (Gimme some crunch along with the flav...) On the other hand it should be easy for players that aren't so interested in the rules to understand the basics, i.e. give a breakdown what strength is good for in the character creation. (Also here it would be great to customize the amount of information - "Strength gives boni to attack and damage. It is the main attribute for fighters." or "Every two points in strength give you a +1 bonus on damage, as well as attack. The attack bonus is calculated as follows: 10 [base] + Str bonus + weapon boni. etc. pp."
What would you like to see? More info and more complexity or simplicity?