Limiting this to 2-D fangames, at this point I think there are at least some that exceed at least some of the official 2-D Sonic games. Note, though, that in the era those official games were made, game development teams were much smaller and so it isn't too hard for a group of fans these days to put in a similar amount of effort; particularly since the Internet allows people to locate each other and find teammates with the right skills.
Broadening it to include 3-D Sonic games as well, the claim that fangames can't possibly be better than official games because those official games have so much more time, effort, and original content put into them--as a result of team size growing exponentially since the SEGA Genesis era--sounds objective enough, but here's something to consider: By that exact same logic, Sonic The Hedgehog 2006 can be deemed a superior game to Sonic The Hedgehog 1991. As I doubt many people here have that opinion, it behooves us to recall that "good" is often subjective and situational, so you really shouldn't reduce it to size alone. Thus from here, let me defend the position of people who feel that some 3D fangames are better than the official ones.
As noted above, I may not be able to declare objectively what a "good" Sonic game is, but what I can do is remind people what Sonic games were like when the series was at its most popular. They featured momentum-driven physics, speed, environments built to use those physics and that speed, point-A-to-point-B platforming, and an increasing roster of characters, but always characters that fit with the preceding points. That isn't any secret to people here, but it deserves to be restated to point out why many people find the official 3D Sonic games lacking--because they have deviated from that standard, and in many regards never actually returned.
Let's look at the physics first. While Sonic did have momentum in Sonic Adventure , I can't remember any point when building up that momentum was a challenge and failing to do meant Sonic couldn't get up a certain place--except for the Perfect Chaos fight at the end, and it felt jarring as a result. Loops in those games are infamously preceded by boost panels and sometimes movement within the loops themselves are completely automated. Other times, like in the aforementioned Sonic 2006, movement in these loops is not automated, so Sonic can just stop moving at all when on them, revealing that his momentum and speed doesn't matter at all; he just sticks to them--which is even worse. It certainly looks worse. The point is that physics in the official 3D Sonic games are an ongoing stream of hoaxes; not always very convincing ones.
Now for the other things. Sonic Adventure added three new playable characters (Amy had been playable before, but not in any Sonic platformer), and one of them was super-slow, had almost no platforming involved, and his goal was to go fishing. It's important to bare in mind my earlier point that bigger isn't always better. Sonic Adventure would be a smaller game with Big the Cat removed; many people would also consider it a better game. Sonic Adventure 2 took out the fishing, but it also shoved Tails into a mech. After Sonic 2006, SEGA started pulling out elements that fans disliked, but they also pulled out things they did like, such as Tails and Knuckles being playable in a similar manner to the way they did on SEGA Genesis. They also made the games even more automated and linear than before, and continued shoving random new gameplay gimmicks into the games to replace those they had taken out.
The reason many people continue to claim some 3-D fangames are better than the official 3-D Sonic games is that these fangames are actually trying to recreate a Sonic experience that Sega just gave up on, and they're actually succeeding at those key things. There are now multiple 3-D Sonic fangames with working momentum physics, and environments useful for testing them. There are at least a few that have Tails and Knuckles playable, quite like they did in the Genesis games. Some have even more characters, and many have fixed the problem originally posed by Big the Cat in Sonic Adventure. Finally, unlike every Sonic game made since 2006, these games are actually fully in 3-D and don't yank control away from players or force perspective to alter. All this might not comprise a compelling argument that these games are better than SEGA's if it was just a matter of some randos finding them more fun, but that's not all it is; once again, the things that these games do are what official Sonic games did back when they were better received. That might not be objectively what Sonic games should be, but it's as close as your going to get to objective, and so long as there still isn't an objective definition of what makes a good Sonic game, you really can't declare people wrong when they say one Sonic game is better than another.
I want to mention that I'm not necessarily expressing a personal opinion in any of the above. I actually don't think making every Sonic character fast and able to roll is an ideal way to give them a moveset (though not doing this does make them untenble for many levels designed for characters more like Sonic), I prefer having more buttons than the Genesis games used, I don't hate Big the Cat, and I can't say I'm one of those people who gets newly excited whenever the next 3-D Sonic fangame comes out that is just a physics demo in a sandbox. However, I also see nothing in SEGA's official (sometimes) 3-D Sonic games that makes me expect them to reach my ideal anytime soon. Fangames haven't, either, but I do genuinely think it's more likely fangames will achieve that sooner than SEGA does, if only because the fans are actually trying.
