I think the bigger problem is that no one ever stopped to say, "who the hell is this Tropper guy and why is he doing this?"
I think people are impressed by Rabbi Reuven Feinstein. It's important to remember this is not R. Moshe Feinstein and being his relative doesn't make him such. He's acting like an @$$ with no judgement by associating with that org.
They could centralize it in such a way that it wouldn't be corrupt. What they should do, but, the reality is they don't care, follows.
As already on the RCA protocols, regions would be created. Each region would have a beis din set up. I would make a beis din for EACH boro, another for just upstate whatever those counties are, another for NJ North, NJ South.... you get the idea... I would say that a Chabad beis din could be set up in Crown Heights and they would not be permitted to use their own regional beis din but they would go through that system.
They should create workshops from the veteran conversion rabbis for rabbis to take if they want to do a conversion. The rabbis would get a certificate or be put on a list to indicate that they had studied conversion with the beis din. The veteran rabbis (who would likely also be the dayanim for the regional baytai dayanim) would also make themselves available for questions to rabbis who had not sponsored m/any candidates before, these new sponsor rabbis. In fact, they should constantly check in with the new sponsors. Women teachers could also obtain these certificates qualifying them to tutor or teach classes. It would be at the discretion of the beis din if a woman had enough Jewish education to take this certification or she needs more study first.
The baytai dayanim could also sponsor workshops for members of the community interested and willing to have candidates over for Shabbos. This would provide a network of secondary support for rabbis who are sponsoring candidates so that they would have somewhere to send them for Shabbosos. These community members would be made aware of things like: you are not supposed to set up preconverts, don't ask them where they are in their process, there is no concrete answer to this question for a candidate, mevushal wine and so on....
In this manner, there would be a balance between the power of the local rabbi and the local beis din. I also think that they could then be practical and have classes set up by the beis din. Each rabbi who is currently sponsoring at least one person would be required to teach X number of classes for the beis din. Any other certificate holder in the community could volunteer to teach a section or more. They would put all these teachers together and have a giant class somewhat like they do at OZ. It would actually be more efficient though, because besides taking the class, the candidate would have a sponsor (whereas OZ has about 60 people in that class and they all have the same rabbi) they are specifically working with. The sponsor would decide when to take a candidate to the beis din. As is the case now, the baytai dayanim would pretty much accept the sponsors recommendation.
Candidates could shop around at different sponsors but, not baytai dayanim.
Because these are all rabbis from the same community who already know each other or will in this process end up getting to know each other, there would be a big difference from what EJF was doing. The biggest problem in gerim is that half the sponsoring rabbis don't know what they hell they are doing and no one so much as encourages them to ask. There is nothing to train them to do geirus and there's no system that pressures them to go and ask a veteran conversion sponsor. Also, if a system like this was set up, Tropper would never have his way. He wasn't a geirus rabbi. He was self-proclaimed.