What, precisely, was the issue with the 2006 situation? Was it literally just that Jonathan Pryce got his feelings hurt? Every year there are dozens of actors who are deemed unworthy of a Tony nomination/win. Is it an insult to every single one of them?
The point of an award is to honor excellence where where it's seen, not to be a participation trophy. Honestly, I WISH we had more awards bodies who weren't afraid to abstain from bestowing awards where they don't feel it's deserved. It's partly this fear that's causing the Tony Awards' significance to become diluted. Nothing enhances the prestige of an award than by sending the message that it's not a done deal; that it has to be genuinely earned.
It seems like a question of setting proper expectations: if everyone is on the same page that the award is only given out when the committee REALLY wants to, and that's a special thing, then theoretically no one will be insulted when it doesn't happen. They'd just be glad when it DOES happen. I'm sure there will be some sourpusses still, but too bad for them. They can get over themselves.
So, having said all that: were there any LOGISTICAL issues with the way they had it in 2006? It seemed like the right idea to set up a separate, smaller committee for it (at least that's how I interpreted the thing I read?). Granted, the smaller the group, the less meaningful it really is. So that's something to consider, but it's not a dealbreaker.
If there's a separate committee of 30-50 or even 100 voters for replacements, it wouldn't be so hard to get them to all the shows. And they can impose a limited on the productions that they have to choose one set of replacements per season to invite the voters to see, or something like that. Since they aren't going to the new shows, then they'd only have to see maybe 15 shows a year, which is more manageable.
It's true that these productions/actors don't really NEED these awards, but like, theoretically that shouldn't be the point of an award. I recognize that it often is, in practical terms, but plenty of people/shows win awards despite not "needing" it, because it's not "underdog of the season" it's "BEST [xyz]" of the season. The point of the Tonys, in theory, is to honor the best artistry on Broadway, and replacements are artists on Broadway.