But if it is too OP compared to the rest, there might not be a choice if gameplay and "balance", should be preserved...
By making it a Radiation Bomb type ability you get enough parameters to change around without a target limit: casting range, initial casting cost, cooldown, channeled or not, AoE around target, drain rate, duration. The latter 3 should suffice to make a powerful but not OP ability.
Belive me, I would love to see these things in game without any Target limit/range limits, I like rendering entire fleets useless!
Phase Missile Swarm wouldn't be OP even if it hit unlimited targets. 300 damage is nothing after mitigation. Same goes for Cleansing Brilliance without unlimited Malice, and that's an ultimate.
while the fleet synergy/unity's presence would be best as passives. Alternatively, depending on buff size, the fleet synergy could be made active, but i'm not sure about that one...
Your "Unity's Presence" is a massive aura, coupled with a debuff aura. Could be used as a non-ultimate with more subtle buffs (movespeed, small repair), but I find the other possibilities and fleet synergy more interesting.
The gravity vortex also seems like an awesome ability if made correctly, but I don't know about combining it with the mobile PJI, I don't think it would be good to put too many things in a single ability, but again, I'm not sure...
It already sucks stuff in, so only the ships that started charging before getting hit would even have a chance to flee. I'm only talking about a localised, albeit fairly large, vortex, it shouldn't be able to cover an entire asteroid gravwell. It would have no effect on ships outside the AoE, while those within get sucked in, possibly damaged/debuffed and can't jump. The shockwave mechanic would ensure you can't trap a 2000 supply fleet for the full duration while peppering it with mines and splash damage.
The "mobile PJI" effect would be like a large, semi-permanent Gravity Warhead, not an Embargo-style shutdown. That would just be an I Win button.