Denny 1 and/or Ghost Fleet "tweak"?

I really like ghost fleet as is, it's just Denny1's superpowers that make it over the top. If Denny1 was tweaked (and our bottom tier caster's buffed) I'd be very happy.

One trick would be to make "the withering" LoS. It keeps Denny1's fluffy ability but at the same time if your opponent is screening their caster behind a jack you can't wither, scourge, parasite and then rifleman them to death.

I also agree with your idea about making Dark Domination 1 focus cheaper.

I don't have much problem with her in isolation, it's just that she's so much better than a lot of Cryx casters. A rebalancing of Cryx casters such that Denny1 was on the same power curve, as the rest of the Cryx stable would be great.  

I think nerfing Deneghra is a difficult issue, because she's so strong that the whole faction is built around her. Changing her significantly would mean that the rest of the faction would have to change significantly to make up for it.

The argument that if Deneghra were slightly debuffed and many other casters were buffed it would balance out--I think that's plausible. But it's still an enormous task and very similar to a full-faction ground-up rebalance, because warcasters are so fundamental and complex.

I really enjoy playing Deneghra because Crippling Grasp, Parasite, Venom, and Scourge are spells that are potent and useful but require lots of thought. I like that she has a really strong spell list and Stealth but is quite fragile and has very little personal threat. It's a great contrast with Cryx's many undead casters who are much beefier.

The feat is nice because it's so powerful, but I feel guilty using it. I feel that, like many control feats, it's flavourful and effective, but it's not fun to play against. Crippling Grasp can take an opponent's model out of the game for multiple turns, but her feat is in many cases a "lose a turn" effect for the whole army, which is the least fun effect in almost any game IMO.

This is hardly unique to Deneghra, of course, as there are many powerful control feats and defensive feats that have a similar result: a minimal, impotent or pointless turn for the opponent (big DEF buffs, big ARM buffs, giant pie plates of terrain, lost actions, mass knockdown/freeze, etc.). Not everyone dislikes them, and that's okay, because they're probably embedded in the game for good. I just prefer soft control feats like Asphyxious 3's (I love that feat!) or hard control feats that are much narrower, like e.g. Venethrax's.

So I guess the obvious change is to remove the restriction on runs and charges (or restrict running only, as per e.g. Icy Grip). Even a SPD debuff is pretty harsh by itself and can still get you the alpha next turn while improving your shooting this turn.

The suggestion of LOS for feat effect is also pretty plausible; Deneghra's hardly braindead to play, and the feat already involves balancing the aggressive positioning to optimize the effects of the feat and risk being attacked, so emphasizing that could work. She'd have to take more risks to affect more models.

As for Ghost Fleet, I think it's important not to nerf it in a way that dramatically reduces the effectiveness of the Rev Crew outside of theme. I quite like them outside of theme, and I think part of the success of Ghost Fleet is that Rev Crew were more powerful even before the theme than people realized. I also like that the theme sacrifices a lot of variety and utility for its powerful recursion and many free points. I've seen some suggestions that are almost there but are probably too much or too little (FA:2 on the crew, which they won't do; making their recursion cost their combat action, which would probably require a significant point drop and require a rebalance).

I've also seen some suggestions that Ghost Fleet is too good even independent of Deneghra, specifically with Coven, but I'm not sure that's the case.

I think the revenant crew need a slight tone down. I would modify Deathbound on the Revenants to destroy the model if it ends its activation outside of command (And at the same time allow returned models to be placed next to the unit commander)

This stops people parking models in deployment zones / so far away that opponents cannot kill the unit which feels abusive to me.

Sure its intentional but its not immediately obvious when reading the rules and the whole thing feels like a technical loophole? (if that makes sense) However I can take or leave it to be honest.

Regarding "seeding" as you put it, well i 100% disagree that its perfectly in line with other recursion mechanics. Theres nothing else really that comes close to the self contained combat action allowed recursion mechanic these guys bring and its shows. It feels out of character/intent to hold models back out of range to take advantage of how its recursion is worded. I dont really think its a big nerf overall but it makes a bit easier for your opponent to take out a complete unit which isnt there currently.