My approach is to set up the bass and the rig together. When the S1 was my primary instrument, I was in a band. The bass and rig were setup such that changing positions on the Q switches would give me an expected change appropriate to the song or passage that we were playing. For instance I might flip a switch right before a bass solo or a quiet passage. I had setups for mellow, slap, etc.
By the time I got my S2 the band gig had ended and my focus changed; I have essentially just been sitting at home practicing everyday. Here again, the bass and rig are adjusted together to arrive at whatever change in tone I am looking for. But the continuously variable Q gives me a much wider pallet to work with.
I've noticed that sometimes I'll love the tone I'm getting, then the very next day, without changes to any settings, I'll find it lacking. I think that perhaps it's like matching the tone coming from the speakers with how I am feeling physically, emotionally, spiritually. Sometimes I'm looking for more warmth in the mid-low frequencies, sometimes more grit in the mid-highs, sometimes a more light and delicate sound, etc. Sometimes I might not make a change for days; sometimes I spend the entire practice session trying to find the right overall balance. And usually I'm just looking to change some very small portion of the overall curve.
And then all that also changes with the aging of your strings; as the strings age, the tone changes, and you have to make adjustments.
I love and appreciate what the S2 offers me; personally, I have no desire to play any other instrument. The tone that this instrument makes possible is, for me, a wonderful gift.
But then that's me. I don't play in a band. The music I'm playing is pretty much a departure from what most bass players are working on. The minute changes I make trying to get the E at the 16th fret on the C string where I want it are not the type of tone issues that someone playing in a band with two loud rock guitar players face.
It's kinda like the difference between Europa and Signature electronics; Signature gives you a wider pallet than Europa, but Europa gives you more choices for quick and repeatable tone changes.
So I suppose it depends on what you want to do, and perhaps on what you might see yourself doing in the future.
I'll add that with practice you'll come to get a good feel for how much a small movement of the CVQ will change the tone; and at that point it becomes as repeatable as a switch.
And again, what the filter, Q switch, and/or CVQ do is very dependent on how your rig is setup. If you flip the bridge Q switch from +6 to +9 with the bridge filter wide open but the treble on your amp is rolled back, then the switch isn't going to do much because that additional bump at 6K isn't getting past your amp's circuit.
Well, those are my random thoughts at the moment. I hope you find something useful in there.