I personally prefer AmigaSYS 4 over any Classic WB install. Its MUCH easier to install on a real Amiga (I'm not a fan of having to mess about in WinUAE). And once its installed its not automatically adding lots of stuff you might not want. Granted Classic WB is perfect for WHDLoad and i'd recommend it if that's all you want (along with some added extras). But if you want to further tweak and add things (or remove) AmigaSYS 4 is much better I feel.
At the end of the day, though, the best system is going to be one you build yourself from scratch. Running an Amiga optimally requires you to understand every single file, script and its placement alongside other programs etc. But when I started on Amiga again after many years away, AmigaSYS 4 was a brilliant jumpstart