One way to look at why deep learning is having the impact it does is that unlike other ML methods, it's actually capable of making use of so much compute. It gives us modular ways to add more and more parameters and still fit them effectively.
First, having 'infinite compute' is a way for researchers to be sure that compute isn't the thing holding back their method. So, DeepMind made a protein folder using all the compute they had available; later others managed to greatly reduce the amount of compute needed to get equivalent results, by re-implementing and innovating on DeepMind's initial write-up.
Second, I think there's a lot of interesting ground to explore in hybridizing ML with more classical algorithms. The end-to-end deep learning approach gives us models that get the best scores on imagenet classification, but are extremely prone to domain shift problems. An alternative approach is to take a 'classical' algorithm and swap out certain parts of the algorithm with a deep network. Then you should often get something more explainable: The network is explicitly filling in a specific parameter estimation, and the rest of the algorithm gives you some quality guarantees based on the quality of that parameter estimator. I saw some nice work along these lines in sparse coding a couple years ago, for example...
Without question, limits exist in every DL architecture; we just haven't taken the time to diagnose or quantify all the limits yet. Now that attention has shifted to transformers, analysis of DNNs' inherent limits is made substantially more difficult, given transformers' huge size. That, and their multi-million dollar training cost likely will make if infeasible to diagnose or cure each design's inherent limits.
Papers say that both are trained on PDB dataset. And still, we see a dramatic gap between old and new Alphafold models. Both were trained by Deepmind, probably with a similar computer power. I think it's obvious that it's not just compute power, method matters a lot.
It's like asking if using the google homepage from 10k iterations ago would perform better than the current version on the present user cohorts. There's just too much invested to justify testing things like that when you can use the time to improve what is showing promise.
I looked through the list of solvers for the protein folding challenges and there were other deep learning, neural network, and classical machine learning approaches on there. Even some hybrid ones! But none of the participants had even a fraction of the compute power that AlphaFold had behind it. Some of the entries were small university teams. Others were powered by the computers some professor had in their closet (!). Most of the teams were dramatically under-powered as compared to AlphaFold. How much did this influence the final result?
What would the other results look like if they'd been on equal footing? Would they have been closer?
It's a genuine question.