For EA it was said it could have been related to Origins initially being the online infrastructure for the Wii U, but Nintendo - supposedly - backtracked. And EA “kind of” punished Nintendo...
Origin planning on Wii U broke down but so did the final specs so even if EA wanted Crysis 3 on it, it wouldn't run. And Cervat Yerli saying that it would is just another one of his lies.
For Square Enix, I guess Sony striked some kind of deal with Square Enix for Dragon Quest XI outside Japan as “timed exclusive” ( that would explain the INEXPLICABLE no show of the 3DS version... ).
INEXPLICABLE?? Nintendo had Reggie parade Dragon Quest around at every interview until it turned sad. "Ho ho, playing Super Mario? I just love to play Dragon Quest on my Nintendo 3DS. I have put over 200 hours in this game fml"
The numbers don't lie, DQ on 3DS hardly sold anything. 3DS is now mainly for kiddo's

When it comes to your point on higher margin products, there is a fine line between trying to make margin and ripping off customers. Ultra Street Fighter 2 is a rip off ! If I was one of the owner, I would ask Capcom for a refund or an exchange with the Anniversary collection.
Software planning is weird sometimes. For launch Street Fighter made sense and maybe the devs wanted it on the eShop but the marketing dudes from Cacpcom and Nintendo convinced everyone to put in on a cartridge so it wouldn't miss the launch.
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