I feel compelled to start with the obvious: this is not a kiddy anime but an animated series for literate adult audiences.
Blue Submarine No.6 tells the story of a water sunk Earth after a madman's having raised the ocean levels and brought about an army of mutant creatures to wage war on mankind. Everyone and everything went under the surface and the battle is fought on ships and submarines.
The creatures posses salvaged technology fused with living organisms whereas mankind employs the latest on on robotics and hydrodynamics to defend themselves from the unrelenting advance of Zorndyke's army.
There is one last hope, a final assault on the creature's pole base but the Blue Project requires the help of a very particular man so they send their best submariner and ship to get him, the Blue 6.
Mankind only see the creatures trying to exterminate them and the creatures only see the men that ruined their world as a consequence of their innate greed. Zorndyke's soldiers, in spite of being genetic experiments, posses reason. Should they be eliminated in the same way they killed 16 billion people with the flood?
Further the 3D CGI, which was quite a novel in 1999, there is more to this series than a flashy animation; it is a twist on the Island of Dr. Moreau with curious characters and very few clichs though there are some.
Range Murata's character designs bring to life the sadness of the people that survived the end of the world and lost everything dear to them thus giving us a miniseries heavily dependent on action rather than on dialogue as the characters are to busy dealing silently with their angst to talk openly about what every one else feels as well; there's no point in expressing it because we already know.
I got to know Gonzo Studios thanks to this and then watched Last Exile, which is superb too.
The soundtrack is based on fusion Jazz, pretty much like Cowboy bebop, and it leads to an interesting aural experience
There are not many shows like this anymore so give it a try, it will do you good.