What sets it apart from others is that level of tweaking and system tuning you cannot do on any other benchmark. While you are right about it scaling with CPU frequency there is certainly a hell of a lot of play to be able to nudge people out with higher clocking hardware if you know what you're doing. It is a time consuming benchmark and probably more frustrating than most others but there is absolutely nothing that is able to replace it. You remove that and you have yourself a bunch of click and run benchmarks.
If anything your sentiment probably applies more to something like 3DMARK05 which is way more CPU dependent than most benchmarks and you are only looking to get a lucky run for max frames without a great deal of skill involved. On the flip side it has a nice gain from tweaking system but yeah still nothing too exciting. Same with 3DMARK03 if you want to go that way and probably 06 as well.
I also reckon some of the newer 3DMARK benchmarks should get a cull before 01 is touched. I'd personally also drop Vantage before others as whatever new comes out is another "vantage" more or less. Keeping a couple of latest benchmarks is also fair enough as that's what tends to always get most interest because of the novelty users.
Unigine is now scaling with CPU as well but at the same time it's stupidly long, has very little tweakability, it's only there because we have bugger all alternatives to Futuremark. Same can probably be said about Aquamark as far as lack of alternatives and why we still hang onto it, even though on the tweakability side of things it is certainly better.