I agree that the initial source of tone is in the imagination and the hands, but the losses through cables and pedals that I hear when things aren't right are not of the type that can be compensated for at the amp, because you are attempting to boost frequencies and properties that are lost in the process. It is more than simply EQ, it is dynamic range and sensitivity as well, I imagine due to matters of impedance and capacitance, and these things cannot be replaced by simply tweaking the treble control of the amp. In fact, all you will be boosting is noise.
There are several solutions to these problems, which include using bypass loopers and dedicated buffer pedals such as the MI Audio Boost'n'Buff, etc, along with careful cable selection. In my most complex rig, I run a total of 13 pedals, but my most 'direct' signal is through only 4 of them, all true bypass, and with a Boost'n'Buff at the end to drive the final cable to the amp. The other 9 are taken out of the chain by the bypass loops. The bypassed signal through this setup remains full bandwidth and punchy, and the loss is kept to a minimum. In this way, the tone that is in my imagination and my hands is what gets delivered to the first preamp tube in my amp, rather than a diluted approximation or distortion of it.
Cheers...................................... wahwah