I have used final judgement only in one case (and found it useful, only in that one case), which goes as follows: I was playing a game with unlocked teams, start with an ally in a 2v2v2 map. After my team had got a difinitive edge (and the other two were moronically fighting amongst themselves), I built up starbases in key allied systems, preparing for the great betrayal! I turned out to be quite interesting to have a fleet prancing from planet to planet (of your former ally's), while having each of the key systems beseiged by SB's of varying strength. The AI of course never saw this coming (moron that they can be), so I managed to fair quite well, knocking out the ally in about 30 minutes of 'heavy sweeping' while only loosing one of the (about) 4 starbases I had supplanted him with.
This is the only case that I have ever used final judgement, and the only time it has proven useful (and against a ally that had any brains it would have been useless, as the SB's would have been long ago detected as the thinly-veiled subversion that they were)... the effort required to construct an advent SB in hostile territory AND upgrade final judgement is simply too great for it to make any sense for any sane player (excepting those who enjoy slow and painful, mocking dismemberment of opponents--in which case final judgement is perfectly suited to your cruel passions!).
I think that maybe scratching it is unecessary, just because it is kinda a neat upgrade in that limited situation that I mentioned. Instead, I think the best thing to make it 'worth while' would be to greatly increase its strength, as I believe Raptor suggested (though maybe not quite 3000 damage..), and ADD a seconday meteor ability that does somewhere from 800-1200 dmg to cap ships (which has also been suggested, I forget where or by whom). This new meteor ability should have a long cooldown time, obviosly, or lvl 10 cap ships would be wasted before the battle was half through. FINALLY, another ability, if the cap-ship meteor isn't to your liking, could be something along the lines of a 'malicious debris' ability, whereby the same 'psionic' abilities being used to direct meteors is used to direct either meteors or debris to damage either ships generally or (and this is the more interesting one to me) specifically target squadrons... the benefit of having it target squads would obviously be that it would knock out two birds with one stone, both upping the usefullness of the meteorite upgrade and increasing the resilience of advent SB's vs. strike craft (another oft-discussed problem with SB's more generally).
Looking forward to thoughts from all, I am sure I have spoken SHEER MADNESS in these suggestions...