In my opinion there's three problems that are intermixed in various measures in dicussions around the EF scale:
1: The theoretical threshold of what should constitute a '5', was changed for no apparent reason other than personal feelings, meaning all else being equal it's harder to get EF-5. I think people sometimes don't grasp this one very well. But even when they do it quite reasonably frustrates them, because there's no good basis for it. At all. And it leads to absurd situations - as Lyza's paper points out, possibly none of the EF-5 rated tornadoes are ratable as such on their structure damage alone.
2: The windspeed estimates for a given level of damage may be too low. To me this is a bit seperate from 1 and 3, in that it's about much more about the fundamentals of damage for a given windspeed. Whereas most arguments arise from damage allegedly being different in intensity to its appearance on its face. This point also has the minefield of the fact structure failure probably occurs across a range of windspeeds, rather than in one discrete 5 mph increment.
3: Bias in how the ratings are done, with a tendency towards nitpicking any given damage indicator towards a lower windspeed due to alleged issues in construction or other excuses, whilst ignoring features that may indicate a higher windspeed. The original EF-scale paper is rather scant in its definitions of what 'well constructed' means, and while NWS personnel will have their own training material that presumably provides more, it's not much good to anyone who can't access it. Furthermore there's plenty of room for personal interpretation as seen by inconsistencies between offices.
I'd say the last reason is the major cause for contention. We sometimes have tornadoes that would have been rated as violent without a second thought before now being EF-3. Even if it's 'correct' (disputable) it's not consistent with prior ratings. If people see a structure rated 'all walls down' when it's been entirely swept away, or see WFOs rate something outside the prescribed windspeed ranges, it's no surprise they object. The last tornado to receive the 200 MPH 'expected' windspeed was Rochelle - a decade ago. Despite many instances of houses being swept away since then, apparently none was well constructed enough to get the expected value.
While you can make the argument that everyone's homes are poorly built, that rather ignores the original intent of the scale (to make an indicative estimate by using a common structure). I'm more sympathetic to the opposite argument. The engineering centred community that has collectively lead to this situation has an unrealistic idea of what 'well constructed' should mean. I'm not saying we need to go all the way back to the anchor bolted = F5 approach, but when the point's reached that the 'expected value' is highly unexpected it's time to start asking whether it's useful.
Speaking of the current system being primarily based on engineering, I personally have developed a tornado intensity rating system entirely grounded in meteorology. Of course, calling it a "system" sounds too formal. These are just some of my personal musings and humble opinions.
From a meteorological perspective, we must recognize that a tornado is, first and foremost, a low-pressure system and a very small-scale one at that (to be honest, this is the root of all its complexities.

If tornadoes were straight-line wind systems with very high wind speeds, there would be nothing wrong with using an engineering-based evaluation system).
In meteorology, the intensity of all low-pressure systems can be measured by the drop in pressure. In fact, this is exactly how we assess extratropical cyclones. For tropical cyclones, pressure is just as important as wind speed, and the same goes for high-pressure systems.
It is precisely because tornadoes have such extreme pressure gradients that they produce such intense wind speeds. However, it's important to note that when the pressure gradient is extremely steep, the strongest winds are confined to an extremely small area, leading to severe undersampling issues with the three-second wind speed when measuring peak wind speeds. In fact, we often observe that tornadoes with smaller RMWs (greater pressure gradients) can cause more severe damage. This is why I sometimes hear people say that prolonged extreme wind speeds worsen destruction—but the correct statement should be that prolonged maintenance of a massive pressure gradient over the same area worsens destruction. On the other hand, a system with RMW so large that it resembles a hurricane and producing long-lasting high wind speeds does not linearly increase damage over time. I believe this is exactly why the IF scale chose to use instantaneous wind speed rather than three-second wind speed to measure tornado intensity. That said, I think using instantaneous wind speed also has serious flaws, as many have pointed out: The duration of a "true" instantaneous wind speed might be so brief that damage may not have time to respond.
Given the meteorological nature of tornadoes, chiefly their extremely small scale and the vast structural differences between individual tornadoes. it can be said that constructing a standardized and precise measurement system, whether based on three-second wind speed or instantaneous wind speed, would be highly complex and difficult (not to say it’s entirely impossible).
To make it as simple as possible, I would prefer to classify tornado intensity by referencing the hurricane rating system. In hurricanes, categories are roughly divided by pressure drops of about 20 mb each. In the Dvorak analysis, 918 mb represents the highest category. Therefore, I would classify tornadoes with a pressure drop of 0-20 mb as EF0, 20-40 mb as EF1, and 40-60 mb as EF2. Lanny Dean previously measured the pressure drops of three EF2-rated tornadoes(contexual damage seems aligned) and found they all fell within this range, including the 2023 Spalding, NE tornado measured by Reed, whose pressure drop was also in this interval. While with little DI for reference, it's true intensity was likely indeed at this level as well.


By extension, a pressure drop of 80-100 mb would represent EF4. Within this range, we observed the Manchester, SD tornado, whose measured 100 mb drop by Tim Samaras also corresponded to its higher-end EF4 contexual damage.

Also within this range, Mulhall OK tornado 1999 was calculated to have 80mb pressure drop within main vortex by DOW Joshua Wurman and the contexual damage it produced also seems to fit in high end 3 to low end 4 level.(by the way, the 3s winds of this tornado would be enormously high and way higher than EF5 standard due to its big RMW and big circulation).

Thus, a 100-120 mb drop would represent EF5, and continuing the pattern, 120-140 mb would be EF6. The maximum would be set at 200 mb, with 180-200 mb representing EF9. Although we don't know whether tornadoes in reality can reach such extreme intensities—such as pressure drops exceeding 120 mb. I’ll set the classification at this level just in case. Also I use "EF" here is just make it easier to read. While it's obviously not EF scale, you can call it whatever you want.Maybe MF scale is is a good name lol.(meteorological fujita scale)
In reality, there is likely a significant intensity gap among actual EF4/EF5 tornadoes, but most damage indicators have already saturated or hit their upper limits early on. Like we already knows that it doesn't take absolutely high end winds to debark a tree or swept a normal house. That's why this system extends way beyond EF5(MF5).
The final rating still should be fine-tuned based on the tornado's forward speed because it's mostly not been considered into the pressure drop value but have effect on damage.
Despite all that's been said, an unsolvable problem remains: it's extremely hard to measure or even reliably estimate a tornado's pressure drop most of time. (Not entirely possible like with the way Sam used here)
This is an unfortunate reality, which is why I wouldn't call this a serious rating system. It's just some of my personal thoughts, nothing more.
But it also make me think that observation and measurement is everything this field need just like hurricanes and any other weather phenomenon.
In the end and foremost, tornado is a weather phenomenon.