I keep meaning to read the comics but then I forget. :/ There's so many of them, although I guess I should just start at the reboot. Everyone I know says it's a higher standard of quality. Plus it will have one of my favorites, Shadow, from the beginning.
The start of the Ian Flynn run is the place I'd recommend to start and probably what is being referred to, not the reboot (which happened due to some RL stuff, and being in the middle of Flynn's run, didn't come with a notable change in quality. Though of course no problem starting there if you want).
The reboot's only had one big arc (made up of a lot of small adventures) and hasn't yet caught up in worldbuilding, though it's introduced a few cool places. Indeed, the big arc in effect deals with the physical side-effects of the reboot.
The pre-reboot time under Flynn's run had a lot of arcs of various sizes (the first story was kinda cleaning up loose ends, but it got on it's feat fast) with some great character moments, and a solid amount of material, though of course there's a few stories that were cut off at the end.
Sonic Universe, side 4-issue arcs focused on different characters, is almost always fun. Also where you'll get the most Shadow. Shadow was originally introduced before Flynn's run, so that's not a worry either way.
I wish Archie would put out more collections, but I haven't seen any come out in awhile so I don't know what's up.