I feel the strategic and commanding advantage of Team Eggman is, personally, obvious. So, I feel Death Battle would likely have Bowser win if:
1. Too large a stat gap to do anything.
2. Somehow unkillable, and they don't (for some reason??) buy Cyber Space, Chaos Control BFR, or Null Space.
I don't at all feel Death Battle reaches conclusions out of malice, or anything. But, I do really hope they fully re-analyze both mainline Mario and Sonic, instead of basically building off of pre-existing research they have. I want them to treat them as if they've never before looked into either franchise, lest we once against have Stadium VS Large Stalactite battle as their peak.
The blood in my body will, in-fact, change state into being a Gas if they once more say that Metal Sonic's copying is imperfect. To this day, I still cannot find a source for that, myself.