It's a various combination of things.
Easiest step is to bring the staff up to scratch on it. Start writing down times properly (they rarely do at Towers), and ensure the rules are being followed (saw mention of people not having the wristband holder with them? Like no guys you can go away). I remember explaining to guests clearly the rules (GS didn't tend to) and most were fairly happy, even if they arrived early and they had to wait.
In terms of limitations it's variable. Whilst the 3 carer rule is fairly useful for groups (we use this to fair affect for example), Blackpool only allows 1 carer per disabled guest. And they don't even have a time card but barely seen anyone else using it on my visits. Perhaps as it's not as openly known due to it being Blackpool? Paultons whilst allowing 3 carers max limits one visit per attraction (or they did when last used it). There are possible solutions to stop the abuse (although 1 ride per attraction is a bit too restrictive in my opinion and could be labelled as discrimination by those arsey enough), but are Merlin too fearful of backlash to make these changes?
Should also be noted that Nemesis is apparently having some issues with non-mask wearers having to sit at the back which in turn prevents RAP users from going on the ride. Which is completely ridiculous.
Though with Chessie the main query is how you apply kids to this if we presume the adult is disabled. They aren't considered as carers so what do you do with a 2.2 family? Or 2.3 if you're Merlin? I've not been in this situation as of yet but that's a potential pitfall.
@Mark9 I remember RAP being rarely used back in the days of working there. Never to this degree of hell at any rate unless you suddenly gained a number of exit passes as well.
But seeing stuff like this is just going to put me off visiting. It's enough effort as it is going to parks with a wheelchair user without having to deal with this on top.
EDIT - In terms of qualifying for the system I'm not sure on the best situation as every disability is different and not everyone qualifies for the same things. Though perhaps with Blue Badges now available for Autism and the like this might be easiest to bring in. Other parks have similar systems (Efteling) and allow doctor's notes but don't really seem to have this problem. And again they don't even have time cards!