If I had to make a thesis for why the manga is so much better, it really is that IDW tries to build intrigue through explanations of everything, whereas the manga tries to reinforce why the mysteries are so intriguing as mysteries.

So the issue with IDW is that it wants to make its own cast of characters to basically be new major Sonic characters They are meant to fit into the games and they are meant to be these long-term characters yuta is not written that way He's very clearly a one shot and he's a guy who just kind of ends up swept up in whatever Sonic's doing Sonic kind of convinces him to be proactive and that is really cool to see Sonic's influence on things like that The most we get from this and IDW was just like Sonic consoling Belle.

Sonic is also written like this much more mysterious character rather than just our protagonist that were supposed to find super relatable and I think that helps with the very paragon nature that the Japanese often prescribe to Sonic. Sonic is also written much more seriously with all of his goofy aspects being quips essentially, here Sonic does some things the main character finds strange but are quite endearing for how goofy they are (like Sonic randomly cleaning the windows of the train).

The manga is not obsessed with taking away this normal life away from Yuta whereas the IDW wants the Restoration because the characters have to constantly be fighting for something.

Let us also point out that the story largely relies on coincidence to get it going while this might seem like bad writing it is actually fundamental to free spirited characters like the core Sonic cast (i.e. Sonic, Tails, Amy) otherwise you get the issue IDW has where it feels the need to constantly tie stories together and introduce a concept like the Restoration to justify even basic things like Sonic fighting Eggman.