Tier lists are highly subjective but as more people make them, you start seeing trends and patterns. That's the data you use for balancing.
For example, the Drover is almost universally cited as S-tier and the best pound-for-pound Carrier in the game. Hammerheads are about in the same boat when it comes to line Destroyers. Tempests are among the best Frigates, Afflictors are among the best Phase Ships, Aurora's are great in the player's hands but sorta meh otherwise, etc. etc. When these kind of observations come up and time and time again, it's a good baseline as to where things actually are. Skills/officers also skew things and some ships, with a bump from Loadout Design 3 (or whatever) can really come into their own.
From the perspective of balance, you should see a bell-curve with a few outliers on the extremes but the bulk of options somewhere in the middle. There *should* be a lot of C-tier ships: good-but-not-great options that fill a particular role or excel in a few circumstances. Personally, I think the curve is skewed to the right with the majority of ships in the C and B categories.