If you give the custom character a good story, it won't be a custom character anymore. At best you'll have to choose between a number of consistent paths.
And i really don't understand the 'give them class, race, skill etc'. The origin characters have the same features than our pc. Astarion can bite people twice a day, that's all. Almost all written lines of dialog are made for the pc, even if origin characters can say it if you made them speak instead of you.
I don't see any trade off between origin characters and custom ones. Except maybe the first have very personal quests, but all the rest of the world is the PC personal quest.
I meant race, class, and skill reactivity - i.e. more options for Dwarves, Halflings, Tieflings, Elves. Right now its skewed towards Drow characters. Also Dragon Age Origins did it well in my opinion with origins. You had starting stories, but you were not defined as Shadowheart the Half-elven priestess of Shar on a Special MissionTM. You could have been a male or female Cousland, a warrior or a rogue, and you had no mission aside from loosing your family and being forced to join the Grey Wardens. It all depends on how much is defined, and not far from being a sheltered kid raised by an old sage Gorion in the library fortress of Candlekeep.
And I don't know how they allocate their budgets. If the origin characters have their respective separate budgets, and the custom character has its own, then there is no trade-off. If there is a single budget for playable characters, then there is a trade-off in how much could be invested in which options.
