Main differences I can think of is Super Sonic, who is my favourite villain in the comics, the lack of freedom fighters (I can only think of seven who have been freedom fighters at all) and the fact that Sonic has no love life like he does in Archie comics.
For a good comparison, you could read the issue where they appear together. Don't remember which one it was, but it was interesting to see them together.
For me, Robotnik has the edge for being able to fully roboticise most of a planet, whereas in Eggman's old world he only partially roboticised some of the Mobians including Sonic and the freedom fighters. If Robotnik and Eggman were in a fight without Shadowbots or Swatbots to help, I would say Robotnik would win
Enjoying crossover. Only major annoyance was when I visited a wiki page a couple of weeks ago to find out the date STH 249 was out, I found the whole storyline on the website so I found out all about Vector, Espio and Charmy's derobotization before the comic had even gotten out. Could be more action with Sonic which I started reading the comics to see, but otherwise I guess things are okay.
Yesterday, Icame on to this beloved website to find I wasn't allowed on it. I had been on several times previously and brought my knowledge of sonic from almost nothing to lots. I went on this website all the time and was so annoyed when I saw the notice. But I realized that it was worth it to see all the sonic comics so now I have. I would really suggest doing it. You can see so much on here and the sign up is so easy. This website has done so much for you to view the comics for free. Give back something by registering to the site. :)