You could have had a cliff-hanger of Skeletor leading a vast Horde army against Eternia, with him cackling and She-Ra still trapped within that bubble that he put her in.
To answer your question, I do think that Skeletor would have made a major attempt to take over Eternia, but should that fail... I think that he would eventually forget about Eternia for the most part (as much as Hordak himself did, anyway - Hordak had thoughts of conquering Eternia from time to time in PoP), and become content in having a planet all for himself.
The rebellion on Etheria would have things a bit better, because Skeletor would probably just be trying to pull pranks on them most of the time (think of how Catra gets on in the She-Ra mini-comics. ).