I went in to school to become an EE so I could build tube amps. One of the big things that quite a few people are forgetting is that a tone stack is what makes each amp sound different (dual rec, 5150, mark IV, powerball, JCM800 etc). They are what make each amp sound the way they do. They are also impedance sensitive which means that they one control can effect the way the other one does, the high knob can effect the way the bass knob reacts and also you change the output impedance on the tone stack by means of the negative feedback loop (presence and resonance controls) which is just a way to change the impedance of the power section. Other than that a tone stack also adds massive coloration to the sound, tube amps are even more mid heavy without it, they take out frequencies that are never cut or boosted regardless of where the knobs are. Some of these frequencies you really don't want.
To see how a tone stack works check out this little program
http://www.duncanamps.com/tsc/ it shows how the knobs effect the frequency response. Be aware that the response of the knobs to the tone are done via impedance and effect the next stages of the amp, this is something that you cannot create with any eq.
but on to what would be cool in an amp
-Built in Tube Screamer with true bypass (Symmetrical clipping)
-External Biasing pot
-A beefed up PT (that can handle higher current for EL34 tubes etc)
-Capable of using any beam tetrode and pentode tube on the market without modification (6L6, EL34, KT66, KT77, KT88, 6550), 20w Screen grid resistors and make sure there is enough space in between the tube sockets
-Power Selection (100%, 50% and 25% (25% in single ended mode)
-Built-in Attenuator
-Plate voltage control (normal voltage and lowered voltage, just like the Recto Spongy/Bold Control.
-Dual Rectifier, Tube and Silicon (with 5AR4 tube)
-Mercury Magnetics Transformers (especially the OT)
-Mercury Magnetics Choke (on off selection for the tube rectifier)
-500v plate voltage (higher amplification factor vs impedance)
-3 tone stacks/channels three knobs with their own tone switches (Twin Reverb or AC30 for clean, Dual Rec channel 2 and Savage channel 4 with voicing/circuit switches)
-The first channel channels has two modes low gain (clean) and high gain. Each mode is just a switch to choose which tubes to use since the clean channel to be clean will only go through the first gain stage V1 and bypass the second stage V2
-5 Band EQ after the tonestack like the Mark Series (located after the Tone Stack but still inside V5)
-Tone Stack bypass
-True bypass FX loop inside the Tone Stack bypass so that a rackmount eq can be used as a Tone Stack or a homemade external Tone Stack could be used. I like the idea of building different Tone Stacks in different rackmounts and being able to switch through different one via loop switcher like the GCX. Tone Stack Effects loop should be located behind the amp.
-Resonance shelf at 400Hz (just like the 5150)
-Presence circuit based on a Dual Rec
-Preamp out located in the circuit directly after V5b with a variable volume knob to control the preamp out level
-Parallel FX loop with wet/dry control.
-Programmable clean boost (up to +20db) right before the V4 phase inverter, have that switchable and call it a solo boost (locate that control on the back of the amp)
-Separate Preamp and Power Amp section Standby Switch so that the Preamp out will work with without the power section being plugged into a cabinet (something I think we all would love to be able to do). For safety put a case lock on the Power Standby (located by the switches) so that you need a key to turn it on, that way it doesn't accidentally get turned on when you don't have a cabinet plugged into it
-Cooling fans (inlet and outlet) to keep the tubes cooled down and ensure fresh air circulation.