There's a few alternative options the parks can alter to improve the system that whilst would have some complaints it's not something that would particularly be a problem in terms of preventing anyone using it.
Main thing is one carer. That's all you get. Perhaps in special circumstances you can have two but that's when you can really go all out on PIP/DLA as the majority of disabled guests will only need the one carer (plus on most rides you've only got two seats in a row anyway). Majority of parks seem to use this so why not ours?
That being said, it would be problematic towards families. But as carers need to be 16+ (iirc) then it's a weird situation. There's some leeway there as things can also be combined with parent swap in order to accommodate some families with it.
Making the system Blue Badge or benefits only is a minefield and should not be considered. Some people can't get benefits but can have a blue badge, and probably vice versa. Hell some severely disabled people are now considered fit to work and have their benefits cut. But that's the government for you.
Perhaps DLP's tiered system could be looked at. Temporary injuries like leg casts have one method, whereas permanent disabilities have another. I've not really used it so can't be sure.
There's no one answer as you cannot encompass every disability under the sun. However it's clear it's an UK issue, as when using it in places like Efteling or Toverland (not Walibi as it's not the best system, though technically the fairest as you stand at the exit for the same length of time as the queue, but with no real waiting areas), as there aren't as many using it compared to Merlin ones. Didn't see many use it at other parks in UK but I wonder if it's as widely known or if the max one carer system prevents abuse?
As for those early morning queues, it's the same at Towers, though at least Thorpe have a separate area. The early morning rush can't really be avoided if everyone turns up on time can it?