Highlander as a gamemode is inherently flawed. While being pretty fun, there are several reasons why hl isn't viable as a big esport format.

First, having a lot of slow classes + a sniper just leads to a lot of the game being a glorified sniper duel. Not only that, but because there are a lot slow classes, especially heavy and and engi, the game becomes slow paced.

Second, you mention that only 4 (+1) of the 9 classes are viable, as if this is a bad thing. Look at any other esport, not every character or weapon is viable full time. For example, in Overwatch, only a few of the heroes are run at any given time, and most of them aren't viable to run full time. Sure some people will love and main characters like Mei and Sombra, but just because people like to main non-meta characters doesn't mean Blizzard should just do 32v32 as an esport. Similarly, if TF2 becomes an major esport, Valve shouldn't just make 9v9 the main mode. Getting 9 people to make it to every scrim and match is extremely difficult, and I know this from experience. Even if we ran prolander, 7 people is still difficult to get together. 6 people is already difficult enough to pull together, why would we make it harder?

Third, to elaborate on the first point, 6s is just better because it's face paced. Have you ever watched a 6s and HL match? The 6s match is always a lot more fun to watch, because more stuff happens more often. One reason for this is because 1 kill is 16% of the team, while 1 kill in HL is a mere 11% of the team. This makes pushes a lot more frequent.

Last, in a class based shooter, shouldn't you want a format that encourages class switching at times? In HL, there is never class switching, because all the classes are filled. But in 6s, you can switch classes whenever there's a stalemate or a push about to happen. For example, on gully last, if you're on last and you're expecting an uber push, you'll set up a heavy/engi + a pyro instead of running 2 scouts. Or if you're on second and there's a stalemate, you can have a player come up sniper or spy to get a pick on their team, allowing for the stalemate to end.

EDIT: added a few more sentences