War Shamblers are often the troop of choice for a variety of reasons:
1- Low resource cost allows more firepower to be generated at speed (at a loss of gold, but speed is often worth it).
2- Size 3 prevents being trampled by size-3 tramplers like minotuars and shambler thralls.
3- The high damage is one of the only Atlantean methods of beating high protection values, often used by players.
The combat program is great, and I love it, but it doesn't tell the whole story.
As for my own Atlantean advice:
War lobsters rule underwater (except versus Rlyeh).
For land battle make War Shamblers if constrained by resources. Make Coral Guard if resources are plentiful. Even though they take heavy losses, always consider the potential of mobs of Atlantean Spearmen.
Spells to keep in mind are: Quickness, Frozen Heart, Paralyze, Soul Slay, and Light of the Northern Star.
For a pretender I prefer the Dagon.
I am not a fan of the Mother Guard, and don't feel that going for a bless effect pretender is worthwhile for Atlantis.
Taking heat/cold +3 was very useful in Dom1 but is FAR less useful in Dom2. In Dom1 most water nations could carve out a huge and wealthy empire in the water. Not so in Dom2. Taking heat/cold +3 will be harsh economically, and I don't suggest it.
Sailors death needs to hit, and then offers a saving throw. It looks great on paper, but fails to impress in practice.
I would never take a god that can't leave the water (Kraken, Nereid).
For long term summons consider winter wolves or sea trolls.
Later in the game if you are doing well, make Kings of the Deep in order to expand your magic paths.
A King that comes in with water-5 can cast Murdering Winter. Always a late game consideration.
Hope this helps someone.