Really, same thing happens to a lot of older games - active servers get whittled down to a few "custom" ones, even though the 'good' ones are still alive, but the custom ones with players in them are often the ones that wreck the balance, add in silly features, stick to one game mod like arsenal, etc.
It's up to the players that DON'T enjoy that to sort of figure out a regular time when enough can log on and start up one of the "good," traditional servers and get it active... and stick to it. Not an easy thing to do at all... but I have seen it done.
I'll give you an example... in Medal of Honor: Allied Assault Spearhead, which is now like 16 years old, there's only 2-3 active servers left that always have people in them. And they're all AWFUL - modded weapons, extra guns, insane gravity, stupid stuff that wrecks the game and is nothing like the original that was so much fun. But they're the active ones...
However, there's still some "traditional" servers that get the old-school, classic gamers and people who used to do tournaments and stuff (rifles only, TDM, etc.) - but you have to know what time they're active. There's one server I like to play in that's literally only active from 1:30 to 4:30 a.m. EST every day, which sucks for me because I can rarely play, but every time I do hop in there, it's the same group of 9-10 players who have found that "niche" of a classic server.
How do we do that in GE:Source with the current player population? I don't know... maybe it starts here on the forums? Figure out who likes certain game types, then have regular times that a bunch of people who like those games types log on? Pick a couple of servers, and everyone knows THOSE are the servers to go to on say, Friday night after 8 p.m., and once we get in a routine, you can always bet on knowing when/where to go to find a non-arsenal/non-LTK game?
No easy answer to this problem... but it's not unique to this mod, that's for sure.