Since this is a ghost-like unit it means; needs to cloak, needs to deal ok damage by itself, needs to have some castable damage-dealing spells (single target, aoe, and aoe/utility). Emphasis is on damage-dealing, not so much on support.
Instead of it having cloak, why not give it a self-hallucinate? It'll always be visible, buut it can look like its a probe, zealot, stalker, etc. (should keep its typical movement speed though).
A lightning rifle that has a single bounce (like muta's, or chain lightning in WC3) would give it some style with its normal attack. Bonus would be to have it's version of 'snipe' be the ability to tag enemy units as kind of lightning rods/conductors...soo its normal attack would get an extra bounce to it. IE; see a SCV line, tag 5 units and the default lightning rifle shot will bounce 5 extra times.
Blink-swap, as an extra mobility spell where it works kind of like blink but it just swaps the location of the protoss ghost and the targeted (enemy or friendly) unit. Unlike normal blink, this would cost mana and shouldn't be castable on massive units.
Now for the Nuke-like power (needs to be built at the academy, costs separate money), why not a sort of orbital strike ability that deals burst energy damage on impact (similar to storm, and slightly less damage overall than a nuke would). Buut after it hits, the area hit generates a temp power radius that lets you warp-in.
Some other notes, I like the idea somehow of the unit maybe having an ability (or its default weapon) bypassing shields and directly dealing hull damage...or maybe having an ability (on a semi-long cooldown) that lets it drain shields from nearby units (friendly or enemy) and convert it directly into mana.
I think you're confusing "ghost-like" with "ghost-copy".
Wasn't saying it had to use all those things, just that those are what make the ghost...the ghost. It is an attack unit with multiple direct-cast damage dealing abilities. The important part is that it deals damage, and isn't support. If as suggested already, the ghost had an anti-emp that healed shields of friendly units it would become an endgame support unit (aoe shield heal is so good it would override most any other uses).
I was reading the posts and i thought: Why not a Protoss Tiara as a weapon, unleashing some mind blasts of psionic energy? Suits better for a female protoss.
About the skills i would focus on psionic stuff as well.
Starts with something like the old queen's parasite, that allows the Protoss Ghost to see what the target enemy can see, like a mind link, as she terminate the link she could deal some damage to the target (Splash damage maybe). As well as the ability to become invisible while not atacking.
Maybe an upgrade ability that allows her to blast enemies back, area or not.
An of course a mana upgrade at the Protoss Ghost Academy
Check that we have some sinergy on the spells here, as she could see troops aproaching with her mind link, get a better position for being invisible, use her psy blast to better position the enemy unit and release the link dealing some area damage.
If someone fells like it is needed another ability, a nether swap (Change position with a target) can give even more mobility to the ghost.
One more spell idea: a reversed Graviton Beam, to bring air units down so other ground units like Zealots and Immortals can attack. This would be way more useful than Gravitom Beam since there are more units than can only attack ground.
I was actually thinking it might be interesting for some of these to show up in the Robot's campaign....
But yeah, right now I have the DT model and Dark Shrine model used as placeholders. I've got to change up the nuke into a proper planet-cracker blast from space somehow, and come up with some sort of replacement for Snipe, possibly that 'switch places with another unit' thing that was mentioned before.
I was also considering swapping the current weapon I've got set up into a more sentry-styled beam, like the focus rifle from Halo: Reach....
I can't figure out why, but the Requierment field for the 'nuke' prep is acting like the Ghost Acadamy's, despite the fact I've set it up to be differently.
Along with that, I keep getting an error when the Sniper shoots in-game, about something being wrong with my actors. (I've admittedly never made a custom weapon before and had no idea what I was doing.... >.>)
However, I did finish up adding in the upgrades. So now we mostly just need a custom model.....