I see, if you say it like that I can understand and agree with your point.
The only difference that still remains is probably my own experience with arena encounters and the strength of the girls I encounter.
Nearly all the Isabelle's I fight are pretty beastly, but this is probably due to the fact that my own Eremia is pretty much stuck at 304k power and I can't seem to get her any higher (maybe some awaken stats and 7* weapon are left, but attribute-vise she hit the ceiling).

And to be totally fair I have to admit that arena is not really my main focus, as I have the tendecy to equally distribute my ressources between all my girls. This is an pretty unusal attempt to play the game, but I like it and my goal is to have the option in the far future to choose any girl I want, without really looking at the power levels.

But back to topic, I think the most common anwser why people would use rather Isabelle than Charlotte even though she is undoubtly better...is the personal taste.
If you have a favorite character you won't exchange them so easily and whenever you get something new, this character will be the first one to profit from it.
Be honest, as soon as the "Gem-System" will implemented one day, you have a character in mind that will be the first one to be upgraded, right?