I'm sure there are Dindrenzi players who say they MUST get rid of the Ablative MAR. Or Terrans who won't field without Nuclear Torps, etc.
I don't see those as essential though to what makes each *work*.
Aquans are still tough without E-Transfer, just less deadly.
Sorylians are odd ducks, benefitting greatly from Weapon Shielding and Shield add-ons here and there. Not sure if that means *essential*. Though i wouldn't use their Frigates (or anyone's where optioned) without Pack Hunter.
Directorate *must* have some upgrades chosen, to either go for an Assault fleet, a firepower fleet, or a cyberwarfare crippling fleet. or to have dedicated element for each. Without that tailoring, they don't do much of anything well.
Relthoza can't run their Stealth game without key upgrades.
Looking at the Marauder preview doc, briefly, there are whole fleets that make no sense at all without using their upgrades. There, options are used to define a ship's role - and without a choice, they have no role.