Although if put to the vote most people would say to remove the Jovian, as with RSV vessels some people own this vessel and we can't really just tell them to go suck it, can we?
Dominion is considered quite good, IIRC. I believe (don't quote him) AndrewChristlieb is quite fond of them in particular, and as far as a support cruiser goes it is generally more useful than the current incarnation of the Mars class, due to battery range drawbacks and better turret rating, all whilst remaining cheaper.
1 per 1000pts seems a little steep, but what about 1 per 750pts as a compromise? That would basically limit you to the minimum amount you put forth whilst giving you more options at higher levels.
Lets face it, the smaller the force (up to a point...) is the more representative it should be of that particular faction/race/army/fleet. At 750pts there should be a noticeable difference in two imperial fleets, and considerably more so compared to chaos or eldar. Bakka, due too its distrust of AC should have a disproportional low amount of AC and a higher ratio of lances/battery. At the really large point values like 2000pts+, the differences between IN fleets should be almost non-existent, because they represent a large portion of what that faction can bring to bear. The current rules somewhat represent that, with reserving and point value limits being less meaningful at higher point values. So although Bakka may not field much AC in general, in a 2500pts battle they will still have a significant AC presence, by virtue of using a significant portion of fleet strength.
This has the advantage of both following the fluff quite well and of giving people more options, and people like option, amiright?