The best in this pack is the original idea. The illusion of the deep is very real, even with a normal land tileset. And having an ocean-life faction opposed to a human one gives the game a lot of spice.
To improve? Some good ideas have been suggested in earlier posts.
Somebody has mentioned the unbalance: the Atlantis faction seems much stronger than the Neptune, in spite of the prowess of the great squid.
This lack of balance happens, I think, because of the ranged weapons of the Atlantis. When you analyse the Glest battles it is easy to see that close combat units are often cannon-fodder, useful and necessary, but ultimately ending up all killed, while the side with the strongest long range warriors wins the day.
The poor fish have nothing to offer in this aspect, and it seems difficult to provide them with any range weapon. A solution might be something you suggest in a previous post: a cute electric eel added to the bunch. Such a beast could throw killing discharges from a distance, thus bringing some more balance to the fights.
In fact I have been trying some simulations with such a unit, and it makes a big difference to the faction. So much so, that I had to limit their power by making the electric discharges depend on ep. By playing with this value (as well as the max-unit) a good balance can be achieved.
Another source of discomfort to earlier commentators is the buildings lack of balance. They certainly are too strong, it takes forever to pull them down. A quick perusal of the values in megapack shows the average ratio of building HP v. warrior attack strength to be about 25/1. In your pack this goes up to 150/1.