For the campaign in question, I'm running one person through a dungeon inspired by Vagrant Story. Clearly some things from the video game can't be emulated, and many of those are integral to the game: ie. the unlocking of special abilities as Ashley (main character) travels deeper and deeper into the city of Léa Monde.
I want to add abilities that will make the character more-or-less gestalt, but there's two problems with this. One: I want the ability to be DM/plot specific and granted. Not just something at each level up. Two: Saves, BAB and skill points aren't on my list as of yet for things to add. Gaining skill ranks from drinking a potion seems really weird to me, anyway.
I've run games before where I granted the party some limited cool and (sometimes) unique abilities and have had some measure of success in balancing them. I know I can include equivalent abilities for the 'really tough' encounters, like the BBEG. Is there a precedent for granting extra abilities to characters as part of story progression in D&D (not limited to 3.5, I can extrapolate) or has it all been unrecorded DM calls? My question is meant for games with a party of six or less.
Playing Baldur's Gate yields very few magical abilities for the main character (especially considering his heritage, for the love of Bhaal!). I want a yard of wiggle room, not just a few inches.