There are lots of nifty ideas that are explored until insurmountable holes are found in them. The two main nonstandard lines of thought that have had any real progress are decoherence, which I'd call a success, and string theory, which I'll avoid rating because I have string-theorist friends but am not a liar. There are plenty of others, and maybe one will bear fruit, but honestly when the next big break comes it'll probably be really obvious.
If one wanted to cast doubt upon, if not "debunk", his idea from the science of the times, it would not have been difficult to do so (see: Tycho Brahe). And that was on an issue that was likely some orders of magnitude less complex than the one we may be facing today. The implication of that being that the "right" answer may initially seem to have more holes than swiss cheese. I think it's very safe to say that relativity, undoubtedly the monolith to which all scientists aspire, was an exception and not the rule in the march of discovery, in its reception/clarity.
It is a hard balance to strike because on the one hand you want to be constantly challenged by your fellow scientists but on the other hand also just take the foolish liberty to fully develop your (most likely flawed) intuition.
So even if I'm highly sceptical of Wolfram he gets my full respect and also Hugh Everett [0] who wrote a letter to Einstein as a 12-year old with Einstein answering: Dear Hugh: There is no such thing like an irresistible force and immovable body. But there seems to be a very stubborn boy who has forced his way victoriously through strange difficulties created by himself for this purpose. Sincerely yours, A. Einstein And later in life courageously confronted Nils Bohr with the [...] idea that the universe is describable, in theory, by an objectively existing universal wave function (which does not "collapse") i.e. Many-Worlds-Interpretation.
[0]https://en.m.wikipedia.org/wiki/Hugh_Everett_III