I would like to note that the reason match and CTF are the most refined gametypes is simply because those are the gametypes that actually get seriously tested. Most of the rest of them are provided as a "If you enjoy this, have fun" design, without worrying about game balance. We are fully aware that there's no way we'll ever properly balance characters in Race, so we don't try.
Also, I highly disagree with your opinion of character balance. In many CTF games I play, I see people playing as all three characters and being a major asset to the team. Sonic is good for getting the flag back, as the thok allows him to outrun the flagrunner no matter what character they're playing as. Tails has the ability to fly, which in many of our CTF stages allows him to fly up to the flag without having to deal with the frequently complicated path Sonic has to take between the bases. Knuckles has the increased fire rate, which is very strong in CTF because most of our stages have massive choke points by design, which give Knuckles a great edge in defending a point. While I personally agree that more could be done, especially to help Tails a bit, in match and CTF all three characters do have a place and I am working to help Tails have his time to shine in 2.0.5.
In Single Player, Tails does tend to dominate, but as a reminder, he also was pretty insane in S3K because of the same abilities. Considering our goal with the single player game is to emulate the classics in 3D, it shouldn't be surprising that the same character balance problems would show up here. Turns out that when you give the player the third dimension, Tails's flight becomes that much more overpowered. Note that when SEGA took Tails into the third dimension, they made him race Sonic, because his abilities kinda nullify a lot of hazards in the game.
However, what this means for the single player is that we need more areas like S3K had where characters have paths to themselves. While there are a few in 2.0, I do hope to have more of these by the time the game is completed, especially for Knuckles. Characters other than Sonic deserve to be challenged to use their abilities too.