Think Naturalize is the way to go these days if you want 2cmc artifact/enchantment removal. Seal of Primordium started picking up steam around the DTT era when Omnitell was the deck to beat for basically the reasons you listed regarding Omniscience and also because you could run it out earlier and make them think twice about putting Omniscience into play. These days though the artifacts and enchantments you want to destroy are more often lock pieces (Chalice, Blood Moon, Back to Basics) and less often win conditions so you typically want your Naturalize effects to be instant speed in order to minimize the window of time you give an opponent to respond.
I can only think of a few situations in which you'd prefer to have the Seal in today's meta game. Maybe against Miracles as an early hedge against Counterbalance or B2B, but overall the instant speed clause seems better than the ability to be proactive with artifact/enchantment hate.
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