The BEST project that CSWR DOWs and scouts are involved with this year is still is not down to ground level with radar scans where most damage happens. I believe they are sampling at 150-180 feet on this storm from preliminary reports. I am not a fluid dynamics expert but I think there are valid arguments for faster or slower surface winds than doppler samples taken tens of meters above depending on vortices, which side of the tornado is encountered, etc.
I am somewhat of an advocate of rating based upon damage potential because it is silly to measure an EF5 over grassland and call that an EF0 if it hits nothing. However, there are many complexities. EFx Tornadoes are not EFx everywhere. They may fluctuate wildly in strength, ground speed, direction with area and that all affects severity in terms of damage potential. We cannot measure surface winds yet with radar or photogrammetry (far too complex and expensive for sub ~20mph accuracy with both technologies right now). Perhaps when RaXPol synthetic beam steered aperture radar is available, it will be feasible to get down to the ground level with radar.
Since so much politics like building codes, warning policy, insurance payouts, etc. can be affected by reporting severity of events accurately (like when is a disaster declared and when not, when is a payout forthcoming and with what restrictions on rebuild based upon building codes, etc.) it seems unlikely and perhaps even unwise to completely decouple from damage indicators.
Personally I would like to see wind speed considered when relevant to damage, and always registered with records when available. This would give us what we need for science and in some cases damage politics, without totally divorcing from the damage indicators method that still has some merit but definitely needs to be updated to consider more characteristics of wind fields and perhaps refine ratings.
In the end different audiences use the EF scale differently, so it will be interesting to see what comes from the ongoing effort to refine it.