For the home versions, I was sadly stuck with the Nintendo Game Boy version. My best friend at the time had the game on his Sega Genesis, and we played the snot out of it.
I never said there was outrage, I said there was confusion, those are very different things. Every single major publication that was covering the development of Mortal Kombat 3 expressed that over the lack of Scorpion.
He was the most played character according to Midway of the original game. This is not something I believe or disbelieve, this is fact. Around the time of Mortal Kombat 3's development, there were legal issues going on with original actors, and it was stated this is why many returning characters had new actors, and was implied as the reason certain fan favourites, like Scorpion, Reptile, and Kitana, were absent. 9 months after launch, all those characters were added into the game via Ultimate Mortal Kombat 3; all with new actors.
Those are the two comics drawn by Tobias, the ones that were advertised on the arcade machines themselves? I don't own them but I have read them, and yes, he wasn't a "primary" character in them, as they were short and they tried to cram in all the characters. Liu Kang didn't have a big role, as I recall, in them either, and he's the main good guy!
Ed Boon stated Scorpion was his favourite character a very, very long time ago, and you are incorrect about the character's popularity at the franchise's beginning.