MT-10 Low/Mid Range Performance

I mean the low range isn't much higher than most sport bikes but certainly beats the R1. The bike is much better at midrange after 6000 RPMs (where it bogs down). I mean I haven't studied dyno graphs of all the different 1000s but to my knowledge there not much debate on how good the midrange torque is on the MT 10

Mine is definitely better after adding the exhaust and tune, but it's still not as perfect as you describe. Did you remove your oxygen sensors or leave them? I left mine on because I wanted to retain the cruise control functionality. They're constantly fighting to lean the bike back out at light/partial throttle inputs and low/midrange RPM's which is what's giving me the poor performance during takeoffs, at very low speeds, and at lower RPM. My bike definitely will not idle along at any speed below 14-15 MPH. I have to use light throttle and clutch slip to maintain low speeds (such as what we would encounter in traffic).

My O2 sensors are disabled by the tune from 2WDW, so they have no effect on air fuel ratio, I also left them plugged in, truely love the cruise control. It seems that a lot of tuners don't get these bikes quite right, likely due to the ETV tables (as mentioned by wintersdark). 2WDW has put in countless hours testing and adjusting the tune and ETV tables to get it damn near 100% perfect. If I'm not mistaken there are over 90 points of adjustment for each gear in the ETV tables, most tuners will not spend the necessary time to dial them all in properly. I've seen many people claming 150- 160whp after the 2WDW tune. For me, the extra power was just a bonus, the bike is indescribably better all around. Smoother:shifting, off idle response and no more waiting for 6k rpm for the power to hit. Power delivery is now linear and noticeably stronger and doesn't fall off after 10,200 rpm. Taken to the limit most other bikes with 180• cranks, will make more peak power, as our beloved crossplanes are not as efficient but they really shine in corner exit speed. Driving4answers on youtube has a great video explaining the benefits of the crossplane crank. 
P.S. In no way am I trying disrespect or insult your tuner, just sharing information as I understand it.

No offense taken regarding my tuner. And I don't think there's that much to removing the throttle restrictions. All restrictions should be removed, regardless of gear. That is to say, no matter the gear selection, the throttle bodies/valves should equally match the throttle tube inputs commanded by the rider. So 20% input at the throttle tube should equal 20% opening at the valves, 50% should equal 50%, 100% should equal 100%, etc. If you look at the ETV tables using Woolich software, you can see how much the throttle valves are opening at a given RPM and throttle input. They should all be maxed out so there's a 1:1 correlation between the two. That's how those restrictions are removed.

And disabling the O2 sensors via the tune/flash doesn't disable them from operating, it only stops the ECU from throwing a code if they are unplugged. If they're plugged in, they're still operating and impacting fueling during lower RPM and light throttle engine operation. For instance, on my GSX-S1000, I had the tuner disable the PAIR valve (Suzuki's name for the AIS system on Yamahas). If I unplugged the PAIR solenoid, the ECU would not throw a code, but if I plugged it back in, it would still operate as normal. It was easy to tell whether or not it was actually operating when plugged in because it would pop and bang just like the MT-10 does when the AIS system isn't plugged, then the popping/banging would stop when it was unplugged and the solenoid remained closed. The software does the same when disabling the O2 sensors. It doesn't actually stop the ECU from using the data they're providing, it only prevents a code from being thrown when they're unplugged and the ECU no longer receives their data. You can confirm this directly with Woolich/FTECU, etc. Checking those boxes does not stop them from doing their thing when installed, only from a code being thrown when they're no longer in place. We confirmed this on the dyno, as well. With them "disabled" but still installed in the exhaust and plugged in, the air/fuel ratio was much leaner than it was when we unplugged them and allowed the bike to run off of the static tune, which was obviously a lot richer than factory fueling. The only reason I decided to leave them on the bike is because I wanted to retain cruise control functionality. I'm starting to think I should unplug them and then go for a ride and see how the bike runs with using only the new fueling tables and not being fought by the data provided by the sensors constantly trying to lean it back out. I'm better it will be much, much better.

2wdw mentioned the closed loop system being disabled, so that the O2 sensors could not affect the tune. As far as having a 1 to 1 throttle, it is my understanding that at low rpms a wide open throttle could cause the engine to bog down, due to loss of intake velocity. As I'm sure you are aware, intake velocity is crucial for torque generation at lower rpms, unlike higher rpms where volume is necessary. The use of the crossplane crank really only has one advantage to the "standard" 180 degree crank. That advantage will not be noticed on a dyno or in a drag race but will be noticed (with a skilled rider) on a twisty road course. The irregular timing of the engines power pulses allow time for the rear tire to recover grip (in between the pulses) which allows for a much faster corner exit speed. This may be the reason the CP4 engines have a reputation for low end power, the ability to add more throttle when exiting corners, while maintaining grip.

Depending on how old, the older cable operated bikes you are referencing. Many had secondary throttle valves that would operate indirectly of the accelerator's input, to maintain intake charge velocity. My 06 SV1000s had this secondary throttle as well as the the timing retard in the first 3 gears. I think the principal purpose of ETVs when paired with an IMU is to allow for the modern features such as :traction control, wheelie control, cruise control, emissions control etc. and as you mentioned, liability mitigation. I for one am grateful for most of thse features but even more grateful for woolich for making them accessible and tunable to the end users.
Once (most) people learn that an internal cumbustion engine is essentially an "air pump", they mistakenly assume that more air is always better, all the time. The problem with that assumption is they completely ignore the importance of flow or intake charge velocity and density. We all know that engines with 1 intake and 1 exhaust valve per cyl (a.k.a 2 valve) are usually better at making low rpm torque. While the the 4 valve per cyl (2 in, 2 ex) engines are known for higher rpm performance. Honda's renowned VTEC 4 valve 4 cyl (auto) engines from the 90s used 2 intake runners for each cylinder, one long and thin the other short and fat. There was an ECU controlled valve that kept the short runner(s) closed at lower rpm, before vtec was activated to maximize flow. When the rpm threshold was achieved, the cam "pins" would shift to activate the higher lift lobe and the short/fat intaker runner(s) were opened to maximize volume.