These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Fridge Brilliance: The Cyber Gang don't seem to care about going back to level 1, implying they'll be unchanged by the game resetting (which is confirmed the next time the game is started), but the Phantom Virus is deleted when they win and the game resets. Why? The Cyber Gang are programmed into the game and thus part of its code and the Phantom Virus is a foreign entity, meaning the game doesn't know it needs to recreate him on Level 1.
Another more thought-provoking example that's doubles as a Mythology Gag, in the original Jaguaro episode, the costume of it is pretty big compared to Shaggy and Scooby and it makes a weird howl. However when the others find the statue it's about the same size as them. If we assume Eric based his research for the game's cyber-Jaguaro off the internet it no doubt is based upon the mythology and the statue and not Barney's costume. Hence why it's size appropriate and growls like a cat and not whatever the hell it sounded like in the original episode.
So Okay, It's Average: It doesn't have a big dramatic Real All Along reveal like the previous movies, and it doesn't have the same kind of character exploration as the previous movies either. But it's still fun, engaging and funny as well. And the cyber environments means it gives the gang a chance to explore places not normally visited.