I personally would prefer it if patents, standards bodies and a few other such institutions were reformed to encourage greater competition and prevent anti-competitive behaviour.I agree. We undoubtedly disagree on what things and in what ways, but I don't think the current systems and organizations are operating at their best, either. On most aspects of the larger problems am very undecided, but I have a particular bee in my bonnet over this issue because I strongly disagree with Mozilla's handling of the situation.
standards were a previously successful tool to avoid proprietary vendor lock-in
They still are. That's why we're talking about a single (albeit broad) format called "h.264", which dozens of vendors support and not dozens of different competing locked-in formats.
but they have since been captured by the very organisations they were meant to regulate
I'm not sure what you mean by this. To my knowledge, the primary participants in the relevant standards bodies have always been the same ones cross-licensing their IP. That would seem to make sense: You can't have interoperable standards if the parties won't share what they have, and the most reliable way of getting someone to share what they have is to give them something in return.
Making any royalty-free standard mandatory (e.g. Theora) is only an issue because of potential patent claims from trolls in general or MPEG-LA members specifically.
I disagree. Making any codec mandatory means mandating risk. In a standard, this means implementors agreeing to take on that risk--but the parties involved in HTML5 have not agreed to take on the risk of any codec. Why they choose not to is irrelevant from the viewpoint of authoring a standard. There is no sense in publishing a standard that is full of stuff which isn't actually standard. Trying to alter reality by altering the spec would not work regardless of patents -- it would just make otherwise compliant parties non-compliant, to no end but smug satisfaction.
(It's worth noting here that h.264 was never mandated by the spec. The parties that implement it have done so for their own reasons, without being mandated.)
Without that patent threat there is no substantive reason to not implement Theora (or any potential VP8 derived codec).
The same is true of h.264, with the essential difference that licensing allows the risk to be managed, even without patent reform. As in, today. If we had to hold up all progress until the messy problems of international IP law had been solved, h.264 would be patent-free by the time we were finished.
And this on top of the fact that there is very little technical or economic reason to implement Theora. It's just not that useful.
the groups who have refused to implement Theora have done so primarily because of influence brought to bear on them by MPEG-LA
On what evidence do you make this claim?