I can understand why people would be concerned about MMR. Personally, if I'd only seen the original research, I'd also be concerned.
Wakefields's study did provoke a lot of thought, such as yours, as to unanswered questions. The problem is, though, that it was a very small sample (a cohort of seven) and made no distinction between causation and correlation. There were other problems with it.
There have been quite a few studies since then and none have been able to show any causation, so personally I'm with those that believe the later more detailed and careful research.
I think a lot of things like this are difficult, and we each have different thought processes. You see, life functions best if usually we take the shortest route to understanding something, and look for the familiar and obvious. That literally saves lives. Doctors are also taught to take that approach as a starting point "Look for horses not zebras."
I'm the sort of person that's the opposite, which can annoy people, but at the same time has my use in contexts where analysis and hair-splitting are useful.
That being said, given that throughout history we've tried to make sense of things, there'll always be a clash between those that have different views on the cause of something. If people didn't challenge the status quo, we'd never learn anything.
I do believe that there are factors in relation to autism that aren't understood and could be. Whether they will be will depend, I cynically believe, on whether anyone (or should I say which big company or government) will fund it. I suspect that given that drug companies probably don't see money in it, research will probably be funded by government in a different sort of country from ours or by crowdfunding or personal sponsorship.
You can tell that the focus of my cynicism isn't so much on the value of research as on which research is carried out and which is pushed by financial and other interests. Not quite the same as your concerns, but not polar opposites.
I went through a phase in the pandemic when I had great hopes that the new long-covid movement, many people working together and liaising with groups with existing problems, would trigger a load of research into and understanding of the aftermath of inflammation. That could help people with a whole range of conditions, physical and mental, especially those that get written off dismissively.
But I now don't think that'll happen unless a big drug company thinks there's money in anti-inflammatory meds, and even then, that'll probably narrow thinking not widen it. And with a government that's made it clear by its behaviour that it's privatising as much as it can of health services, there are a lot of conditions, not just those with an inflammatory effect, but others we don't fully understand, like autism, that are seen as too expensive or too much hassle to treat. (Unless you can pay a private company with friends in parliament to lock people up.)
Random example of area of research that had support then lost it politically - certain politicians such as IDS got terribly interested in epigenetics when it suited their idea that benny-scrounging chavs (other insulting terms are available) were changing genetically to become lazier or more antisocial or whatever, and that they then passed this down the generations.
There were problems with this notion, not least because it then poses nasty questions about how far politicians like that would go with eugenics. But it's all gone quiet on that front publicly - maybe wasn't as useful to those politicians as they hoped?
So research into not just our genetics, but what triggers particular genetic traits could be really helpful yet really dangerous. And that's not the only sort of research one could say that of. Ugh, messy.
Which brings me back to autism and MMR. I remember how much impact it had on me when I encountered a fight back of a different sort. Neuroatypical people speaking out with a challenging thought I'll encapsulate as "So you think autism is worse than death?" I thought how if I had a child, I'd prefer autism to death, but I'm not sure how I'd feel now thinking of how our society treats people with autism and similar & related conditions.
After all, a challenge for you and me - where MMR is given, parents are more likely to complete the course than if you give the three jabs separately. Each disease carries different risks. Maintaining herd immunity against rubella protects mothers from it, reducing the number of deaf babies. Hmm. Deafness versus autism? Well, you'd be in a better position to compare which people get treated worse by society. And that's without considering the level of risk, or risk of other conditions, or even that when you choose whether to have your baby vaccinated, hopefully either way, you're there to fight their corner whatever the outcome, but if you reduce herd immunity, it's someone else that has the problem. Ah, but if it's your baby that has the problem, what if you can't look after them? Still someone else's problem.
Aargh! So as I say, whilst I disagree with your interpretation of the overall research into MMR & autism, I think we'd agree that these are horrible decisions for parents to make.
I use that as an example of how whilst I disagree with your interpretation of the MMR & autism research, I think we'd agree that there are always lots of vested interests when it comes to looking into things like causes, triggers, treatments etc. of health, impairment & difference issues.