Those damn bears!  Yeah good point about the counters to.  They are there but are so weak as to be called counters.  From the top of my head:

Curse or Elemental Attack/Spells vs High Armor

Doge or Blind vs Maul or low accuracy hard hitters

Single Unit vs Overpower

Spear vs Counterattack or High Armor

Haste/Slow vs high initiative

Elemental Attack vs Low Elemental resistances

Anything vs Ranged (definitely need a buff)

Fireball or Splash vs Groups

Regeneration + High Armor vs soft hitters

Maybe 1 or 2 of those can be considered a true rock, paper, scissors counter.  The rest are meh, which means you can just build a generic super unit to take on everything (boring).

I think monsters should generally be harder but the lower end to have some fundamental massive weakness(s) to force you to adapt to your surroundings.  There is very little adaptation at the moment.  And then have large rewards for building certain unit / researching certain spell for killing the monsters.  

This feature is what Master of Magic used to have--very tough battles with high level monsters that you can win early on with the right counter (which is not immediately available) with a reward which makes the beeline for the tech/unit worth it in the end.  I think this is the only way to increase re-playability on this front as you cannot just use any generic strategy to win (which you can at the moment).

Anyone remember the phantom warrior spam vs those pesky Earth Elementals, etc?

Each to his own I guess.  I personally like rock, paper, scissors as I think it adds more strategy and punishes crap strategy but it's personal preference.

Sample suggestions for variety (using Hoarder Spider as example):

Giant Hoarder Spider (+50% hp)

Fast Hoarder Spider (+5 initiative)

Venomous Hoarder Spider (extra poison damage/turn)

You can be very creative on this front and don't need new models.  You can even just colour the old models like the current shrills. :/

Lightning Hoarder Spider? (okay, this is going a bit far).

I am not impressed when I see this list, mostly due to the inability to correctly acheive half of the items unless you are the correct faction. Blind and Curse are both Empire specific. and Single unit vs overpower begs me to have very overpowered heroes or ignore the creature, I cannot produce proper "single units" to use which I think is a bad way to counter something.

Spear vs counter attack... How often do you see counterattack in the wild? dogs and wolves they are so squishy it doesnt matter.

There are a couple of ways to deal with high armor, tht is nice, though elemental attacks are rather weak IMO and I usually ignore them unless I get the elemental damage in some package of good stuffs on a weapon.

As with the other counters, there are these soft counters that are more like "incase you have fireball, press the fireball button now" rather than I would tailor my army for my opponents weaknesses, I cannot possible retrain my trained troops to use different weapons or give them any of these abilities, besides shields and spears. (Depending on faction again).

I know heroes can counter most of the things you meet in the game, so meaby the game is less centric about trained units than what I would like, just my feelings anyways.

Sincerely
~ Kongdej

Ah, Civ IV, we shall not see your like again..

That said, I agree with Kongdej and MiamiBigAl, Fallen Enchantress doesn't allow trained units to shine against monsters, or even against AI troops at higher difficulties (hard to counteract x3 HP on the enemy)

My solution would be more traits, including some that would be absolutely overpowered if they were available without research.  There could be traits that simply negate 'overpower' for example, or that have dodge bonuses against 'circle attack'

I honestly dont like all the "negating" going on, id rather have traits that defend against maul, and defend against overpower.

Sincerely
~ Kongdej

and pretty high-tech compared to bears

Sincerely
~ Kongdej

Malsqueek -

Those are some great ideas. Another possible addition:

5) A trait where you get a bonus against enemies with higher initiative than you (an opposite finesse trait - call it stalwart or something)

CM

I dealt with maul last night using standard trained units.

A wandering juggernaut approached one of my best towns when I had no heroes or trained troops around. I had 2 militia plus one archer, and 2 turns to prepare.

I designed a unit with warhammer, round shield, and the 2 +10 dodge traits. I rushed 2 in those 2 turns, and cast evade on them both (3 air shards). I didn't bother investing in defence as it wasn't worth it, so just wanted my most damaging weapon and as much dodge as I could muster (I think it was about 35 in the end).

It did the job, I lost 2 militia and one trained unit but killed him. I dodged enough times to outlast him.

80 mana points for two casts of "Call to Arms"?