Overall there has been quite a few religion threads in the past and only a few discuss champions/villians/saints/etc. but in passing.
One thing that could make religion more important is that gods and demons can choose a champion to represent them if they don't have a physical form. These champions can go from being a regular peasant npc or player character to a hero/demigod status. Besides the overall stat boost these individuals could also have their skills boosted equally across the board--or like in creation menu--dump points into already strong skills to become even more powerful, and/or boost there weaknesses so they are less evident. The skill boost allocation can be attributed to the god in question.
These champions would have markings to signify their covenant with the deity. These can be marking such as stigmata, tatoos, extra body parts (a third eye), etc.. This can make the champion recognizable wherever they go, both adding and hindering them. Champions aligned with a god of a local religion can be welcomed by the villagers, unless the religion is of a demon that terrorizes the region. this could work out in that the Champion can approach otherwise distrustful settlements and be welcomed immediately, unlike having to establish a baseline trust, and be bestowed armor, food, water, liquor, and other gifts. On the other hand a alignment with a demon/evil god could make any villager hostile. The villagers would be resentful/paranoid/ fearful of the champion. They would hide indoors, lock doors, run into the wilderness, make sacrifices to the champion to be spared, etc. However, the current game probably wouldn't support this as npcs will attack almost anything hostile to their civ. Here is a thread that explains the trust/fear aspect and its implementation:
http://www.bay12forums.com/smf/index.php?topic=105400.0.
Overall the champion can lead to whole levels of fun. Depending on alignment the champion may rise to be a great military leader and have many followers to fight the forces of evil in a mighty crusade. The champion could help conquer entire regions in the name of the religion, defend the region from external/internal force, and/or fight the legions of night creatures, titans, and megabeasts.
Inversely, the champion of demons and mad gods will not seek out followers from villages and forts of good alignment. Instead the champions minions can be recruited from night creatures, titans, megabeasts, goblins, necromancers, witches, and devious humans and elves through magical and blood pacts. These armies of the damned can be used to spread fear and terror across the different civs. If enough bloodshed is spilt--through battle, massacre, sacrifice of prisoners volunteers--the demon/god may be summoned and brought into the world, rendering a great cataclysm.
Over time the champion may have enough of a following to become the ruler of the region in question and may even be seen and worshiped as a new god--to the irk of the god(s)/demon who bestowed the powers. This can set up interesting betrayal set up where the god can curse/banish the champion making them the evil that they were sent to destroy and/or the champion can rise and usurp the god/demon and banish them to the earth.
An interesting aspect of this would be that the player may not be the main focus. Instead, as in Oblivion, the player is merely a companion of the champion--following them into battle, transporting orders and supplies between camps/towns/forts, retrieving holy/tainted relics, etc.. The player would almost be a bystander able to sit back and watch the world change and form.
Whether or not the player is a champion there can be pitched battles between good and evil champions and their amassed forces. These battles can possibly determine the future of entire civilizations and the outcome that the world will become. This can create a great importance in fighting as the fate of the world can be at stake. But players and npcs should have the option to be separate from the conflict and not even bogged down with the dichotomy of good and evil.
Furthermore, champions may have artifact weapons and armor of great power and ability. Crusading champions may have holy blades and armor that dispel and exorcise the evils of the world while a demon follower can have weapons and armor that taint the air around them, driving those around them to madness, and melting them into victims into
magma/acid/syndromes fun piles.