If you like any of these then feel free to use them

Ok so you go into the random map generator, place a 'tiny' ant mound (Of 'red,black,army,or wood' ants) that if left alone long enough or kills enough food for the queen becomes an ant mound then a 'large' ant mound which allows the ants to split and produce additional mounds which continue on growing & spliting indefinatly or until defeated by nearby mound of same of different type of ants or any number of other foes.  Choosing to 'feed' the mound(s) could allow you to eventually use the ants as mounts.

Or perhaps go into the random map generator,  place a bandit camp which through killing (or by 'assistance') would grow to bandit stronghold then to a bandit fortress creating a bandit lord that would establish more bandit camps in an attempt to gather more power.  Once the new camps grew large enough to produce more bandit lords they could either join together creating a bandit king (uniting the bandit factions under one 'banner') or turn on one another in an attempt to gain territory or at least knock out the compitition.  Befriending these bandit lords or the king could allow for them to operate in your territory unhindered & possibly grant you a bit of coin for each succefull battle they have.

Would also be neat if some types of creatures like ants or bees that produce pheromones would do so when they attack or get attacked that would pull all others in nearby area to come in for the kill gaining a bonus to attack due to the frenzy.

What about something like ant lions that as they spread, each digs a cone shaped hole in the 'sand' that any one of a group of passerbys could fall into giving the creature a chance to snag them up or pull them in and gain a big bonus to battle against the 'caught' unit (if the snag attack was successfull).

Oldie but goodie, werewolf or vampire attacks unit giving chance for unit to become cursed (If curse occurse in victum before death of the attacking 'werewolf' then the unit joins the attacker as one of there own.

One walks into a forested area and is attacked by a 'living' tree for disturbing it's rest, or when attacking something in the forested area one gets attacked by the 'living' tree directly afterwards for disturbing it's rest (Possibly hitting you while your injured)

Have slims in the swamps that multiply when hit by edged weapons but die when hit with blunt or fire weapons/spells (Stolen from d&d but neat idea)

Rust monsters or something that instantly destroys metal weaponry or armor, but easily beaten with wood weapons (Also d&d)

Not sure about the future water battles & such in E:FE / E:WOM but the hydra that gains another head (attack) per winning battle/getting a kill or could gain a head due to edged weapons cutting head off allowing for two to take it's place

Possible guardian type:  The Madusa/Basilisk, gaze attack that turns unit hit to stone or petrification

Quest: Mirror of many destinies (or whatever) - upon finding this hut you find an object in the back of the room covered by a black tapistry, after removing the cloth you discover it is a mirror, look into mirror - yes/no..... after looking into the object your party/unit either are imprisoned in the object until the next part of the quest is completed that releases your units, teleport to another location on the map, or an imprisoned spirit offers you some reward for freeing it by completing the next part of the quest.

Quest: The hunt for karma - send in as many semi-decent ideas as you can in hope that someone will find one worthy enough to grant thee a token of awesomeness.