I agree on the saves for the ships. 4+ in a vacuum is not horrible. However most things that are shooting at it other than basic ranged weapons have at least -1 rend. This leaves the ship with a very paltry 5+ save, with no access to a ward save.
I have always said that they just need to give all the ships the batten the hatches rule from the Ironclad. But making it a +1 to their save, rather than re-rolling 1's. (Its not like we have any other way to get +1 save). We of course would keep the rule about disabling embark/disembark.
Then change "Prove your Worth" to give one attack profile get +1 to hit for all visible vessels.
Also, Arkanaut companies need to be 100 points. with 12" range, they are not really any different than many other melee only units. The main downside is that they cannot use their damage dealing equipment every turn.