Because they're simple references. There's nothing deeper to it. It is not really any different from this twenty years ago
Except now it's a Disney movie and has John C. Reily in it.
Writing video game humor is hard. You can't make it too esoteric, but making it too broad dilutes the point. The easiest route to go is just pandering. You know who no one ever sees anymore? Q-Bert! So let's represent him as abandoned and in need of food. That's easy to do and people will get it. Why is Zangief in a villain meeting? Because he has a Russian accent. Simple.
I'll see it, and will be happy to admit I'm wrong, but at every junction I have seen this movie since it was rebooted, I have been pretty unimpressed. Like I said, writing video game humor is hard. The easiest path doesn't impress me.
I was hoping for Who Framed Roger Rabbit for video games. That movie was more than drawings representing Mickey Mouse and Bugs Bunny in the same scene. It was Mickey Mouse and Bugs Bunny, the characters, in the same scene.