You've pressed one of my hot buttons with this post. Of course you should have tone controls; that very few higher-end units (preamps, integrated amps, whatever) come with them anymore is, IMO, one of the consequences of audiophile pretentiousness that only benefits the manufacturers. Is there a degradation in SQ when tone controls are engaged? Maybe, a tiny bit. And yes, we're perfectionists. But can you really hear the difference? Try it was a unit that has a bypass button: set the tone controls to flat, then use the bypass to judge the sound with and without routing the circuit path through the tone control pots.
Here's the thing. Mahgister always advocates for rigorous (some would say obsessive; check out the photos of his system!) room acoustics treatment. Yes, room acoustics are hugely important. The room is one of the very most important components in your music system, no question. BUT...not all recordings are created equal! Tone controls give you the option of adjusting for a recording that is harsh in the upper midrange, or lacking in bass, or a host of other deficits that would be, shall we say, grossly inconvenient to do by re-arranging one's entire acoustic space for each new piece of music. Someone said in this thread that doing so with tone controls is just playing recording engineer, implying that it's a childishly naive thing to even wish to be able to try. Fine; be that way.
As for the "loudness" control, yes, there's the Fletcher-Munson curve, if you want empirical support for the usefulness of this tool. Of course, good tone controls will enable you to do what a loudness button will do. By "good" I mean something like the "semi-parametric" tone controls on the NAD 7600, which allow you to select three different frequency ranges with a toggle switch that can then be dialed in with the bass or treble pot. Another approach is three controls, like on some of the Marantz integrated amps.
One more thing. IMO, micro-adjusting the balance is very important for fine-tuning the soundstage. Therefore, I consider a powered balance that can be adjusted from the sweet spot using the remote a necessary feature of any amp; I would not consider an amp that lacked this feature.