Eclipse is too much.
Phase ships with unconditional movement abilities are not okay. Phasing is already an extremely powerful movement option that renders torpedoes as an assault option moot and forces you to pressure a ship while it's in p-space to actually get your torpedoes to land. Phase skimmer gives the eclipse a get out of jail free card even if it runs its flux really high while phased: one of the key ways you're supposed to deal with phase ships, theoretically. Phase teleporter would be a more reasonable option for an ability.
Phase ships with a shitzillion ordnance points are not okay. All ships have to make sacrifices and they can't have everything. If a ship has great base flux and/or shield stats it has to have low op to make up for not needing things like the flux mods, hardened shields, etc. Doom has great base flux stats and comparatively low OP. Brilliant has okay base flux & amazing base shield stats and comparatively low OP. Dominator has mediocre base flux and terrible base shield stats so it has a shitzillion OP. Eclipse has great base flux stats; Giving it tons of OP on top of that is too much.
Phase ships with comparable mounts to ziggy at less than half the DP and more than twice the base speed are not okay. The Large mounts even have a decent turn radius. Not even ziggy has a good turn radius on its large energy mounts. The only other cruiser with 2 large mounts in the game-dominator-has almost no articulation on those mounts and they're really far apart so it's difficult for both mounts to get a bead on a small target simultaneously. Eclipse can focus both large mounts on one small target so it gets to autodelete frigates for free. Even eradicator, one of the premier hunter killer cruisers in the game, can only do so with medium mounts. That's to say nothing of the extent of the pressure it puts on ships of equivalent size. Capital grade firepower on what is effectively a fast cruiser with phase capabilities must have drawbacks. Even just 1 large mount would present a considerable amount of pressure let alone 2.
Unrelated, but from the same mod. May be of interest to you.
450308 [Thread-3] INFO data.scripts.bounty.MagicBountyCoordinator - Corrected trigger_playerRelationship_atLeast 'Tritachyon' to 'tritachyon' in bounty yunru_libra.
450313 [Thread-3] INFO com.fs.starfarer.loading.LoadingUtils - Loading JSON from [data/config/modFiles/magicBounty_variants/libra_hull_Assault.variant]
450315 [Thread-3] INFO data.scripts.util.MagicCampaign - could not load ship variant at data/config/modFiles/magicBounty_variants/libra_hull_Assault.variant
450315 [Thread-3] INFO data.scripts.bounty.MagicBountyCoordinator - Missing fleet_flagship_variant 'libra_hull_Assault' from bounty yunru_libra. Bounty is INVALID!