i agree with most of what you put in there, and it doesn't seem that ludicrous to me,
bomber script is controversial as always , i wont comment on that
about Atlantis, i think that it firing from underwater may or may not be a good idea, i'm not sure about that one
what i would have done is buffed the AA on it to a reasonable amount, like 600-1200dps (1-2 cruisers worth), i think over 800 may be a bit much
reason for this is i think that it would look silly firing from under water :/
and one cruise doesn't make that much difference if there is a lot of air concerned, so it firing from under water would be just slightly annoying and just seems unintuitive to me
(only unit that can shoot at air from underwater)
currently it has 320 dps vs 500 from cruiser
http://faforever.com/faf/unitsDB/unit.php?bp=UES0401,UES0202