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.
Ho Yay: Dr. Wily with Dr. Eggman. Not only are they buddy-buddy in the comic proper, the "Evil Friends Forever" variant covers go out of their way to show the two men just having a jolly good time!
scans_daily seems to think this is going to end in the best comic book wedding in years.
In Sonic the Hedgehog #248, Eggman acts like a jealous girlfriend when first hearing about Wily's history with Doctor Light, with Wily having to reassure him that while Thomas may be brilliant, he's nowhere near as brilliant as the two of them are.
The solicitation for Part 8 even refers to their relationship as a "bromance".
I Knew It: Quite a few fans guessed correctly that Robotnik and Wily were going to have a nasty falling out.
Moral Event Horizon: Dr. Eggman and Metal Sonic cross it by trying to toss Dr. Light out of the Skull Egg to his near death. Even Dr. Wily thinks that they went too far and it cracks their otherwise powerful new friendship.