Abilities are fun, numbers are not
Ok, I should begin by apologizing for making such a general statement, but I'm just not in the mood for writing another wall of text. But that is the gist of it: unlocking new capabilities and abilities is more fun than getting bigger numbers. One of the problems with Galciv2, in my opinion, is that it was all about numbers, from research and civ costumisation to planetary improvements. Gameplay is about interactivity, and interacting with numbers is called mathematics; I know that some people enjoy number-crunching, but personally I perfer clicking a button and having something cool happen. So, for instance, instead of giving my sovreign a 10% bonus to production, I would prefer having a one-time special ability that greatly boosts production in cities for a limited time; in the game world, this translates as my sovreign's genius leading to a temporary golden age, during which my civilisation constructs wonders that will never again be matched. Same goes for combat: adding +1 to the attack of my sovreign is pretty dull; how about giving him a special ability instead, like a sweeping attack that flings several lesser units into the air. Same goes for civilisations; I would rather have my guys be able to do something cool that no one else can rather than give them a numerical bonus. Brad has also mentioned wanting cities to be unique, which is something I greatly hope will be successful, as there is nothing more boring than an empire consisting of cloned cities filled with +10 Mines of Production (as was sadly the case with most of Galciv2).
Overall, this has two main drawbacks. First of all, creating special abilities takes more dev time than assigning numerical bonuses, which is related to the second drawback, that such a system takes more effort to mod. However, in the end I believe that the game would much benefit from this, as this goes in the stated direction of "giving the game a soul".