Some great ideas! Epic Wins! 
A living world. Creature evolution. Organic growth. Always a different world, naturally.
?? Creatures level over time + combat. A creature of appropriate level, having meet a series of requirements, rolls for hero mini-boss status (those who can lead). Have mini-bosses attract bands that either roam or settle depending on their nature (+ game triggers and RNG rolls). At various triggers, a mini-boss led band establishes itself as a Minor Faction. Colony reaches a specific size, then auto-builds a building, which auto-builds units every N turns. Mature colonies have a variety of buildings, producing different unit types at varying speeds. Colony grows as units amass to then disperse in banded waves of havoc causing fun. At a proscribed colony size, the mini-boss seeks out a secondary site to colonize. Perhaps less intelligent creatures can spawn a per-species version of pioneers.??
?? Allow creatures of like class to breed. RNG rolls for stat and ability combos. Allow for variety, resulting with some rare uber-spawns (up to mini-boss status). Allow mini-bosses to breed with other creature classes (within classification limits?). Allow for the evolution of hybrid species (Griffins, Chimera, Spider-crocs, toothy frogs, and more). Give mini-bosses variable and RNG affected objectives: find a mate, form roving clans, form colony, destroy budding civilizations, seek to unify clans, and so on. The breeding of mini-bosses might result in the ultra-rare Big-Boss. The big-boss possesses a few ultra-uber stats and unique abilities. Under special conditions a Big-boss can establish a creatures version of city. A serious of events, fulfilled requirements, and RNG rolls can bring rise to a limited monster civilization (rare, but with increasing odds and triggers over time).
?? Some Big-bosses from certain species, can engage in diplomacy with other monster clans; as well as with applicable Kingdom and Empire leaders. Small monster bands can form clans, which can join with other clans to create a greater inter-species alliance. Players can attempt to ally with, or otherwise manipulate creature bands/clans/alliances to their benefit. Kingdom and Empire to have their own potentially friendly creature sets. Player (human and AI) can expend resources to covertly assist a monster group in the harassing of an opponent. Or can attempt to openly ally with it. Constructive relations between Player and certain creature classes, might trigger aggressively hostile relations with opposing creature classes (natural enemies). Player/creature relations to affect diplomacy modifiers between players. Player decisions to affect existing creature relations (torch a forest after chucking a fireball at an enemy, and risk having your Treant allies turn against you).
Countdown to Monster Armageddon.
?? Like sand through an hourglass, the passing of turns is a countdown to monster Armageddon. Creature activity and intensity increase exponentially over time. Building up to a powerful creature end-game. Ignore creature expansion at your own peril! Or, act to quicken monster meltdown towards your own risky aims. Left alone to its evolutionary device, the more breeding creatures there exist, the more likely the spawning of rare uber-beings there will be. While over time, and impacted by global events; various creature triggers can be increased, as the odds against uber rolls decrease (bigger bosses, more of them, and spawned quicker). A countdown towards monster armegeddon has begun! Player actions can impact events towards keeping the monster armageddon at bay; or they can conspire to see it quickened. [See the brilliant Armageddon Counter in the Civ4:FfH2 mod].
Due to a series of RNG rolls, some games will develop to be creature intense sooner than others. In some games, numerous roving creature bands may thwart aims towards conquest.. as armies are ambushed by great bands of berserker beasts. While in other games, a Sovereign is pestered by the constant spawning of weak though numerous, little green meanies. And from time to time there may emerge insanely powerful beings which might require an alliance to defeat. While some rare games will see the rise of powerful creature alliances which will break player preconceptions as to how the game is played. On a per game basis, the level of creature danger becomes dynamic. You never know quite what you will face, or how exactly it will evolve. But as player, you will have opportunity to read your world, and make decisions which have impact on an eventual creature population explosion... and everything that goes along with that (including increased odds for uber-being spawns, an increase in creature related triggers, a more rapid rate of creature leveling, + ).