The only recourse we have for things like this is by making requests via Meta SE. I'm not a huge participant there but I do glance through and read questions semi-regularly. Before I jump into what I see the issues there being for us...
Does anyone else feel like this will be a problem for the site going forward?
I feel it's already been a problem. We have never had enough people with close/reopen voting privileges, etc. That is partially because we also have a problem getting members to participate in the system to the extent that they already can, e.g., by upvoting and creating more high rep users. Making it a difficult ediface to budge.
Put another way, the site has some peculiarities which make the one size fits all deal particularly awkward. However, most of the community on Meta SE isn't from here, and there's no real reason for them for them to be sympathetic to our peculiar problems.
Of course, this problem is not so peculiar that it only affects us -- but I think many or most of the other sites it affects are still in beta. We did not graduate because of our stellar leaderboard. To be sociological, taking this problem to the SE community at large means running into the inherent conservatism of any community, namely, if a problem doesn't affect most members but it does imply the entire group has to change policy, they will tend to take this as an affront and respond that they haven't been wrong up to now and therefore there's nothing wrong with the way things are now.
On the other hand, since the policy around graduation recently changed,1 and this change is no doubt part of why we did graduate, we could in fact be considered an exemplary case of a site which deserved to be graduated under the new policy but that makes apparent the need for some more policy adaptations.
Someone already brought this up for discussion in pretty much that form several months ago:
The response was pretty underwhelming, which is still better than "overwhelmingly negative", but it does imply there is not enough interest for anyone in a position to act to take notice.
Anyway, the discussion seems to have stalled at that point and the best place to start would be to pick it up there. It could be something that will become more of an issue if a wave of similar long term beta sites are graduated.
So, not an impossible goal, but don't hold your breath or get your hopes up. Based on this question and that one from Meta SE, the focal points of the issue might be:
That the jump from "beta" to "graduated" thresholds might be better done with a scaled system than involves saying we want/need a certain percentage of overall users with certain privileges, then set the thresholds to achieve this.
A point of resistance to this is fairness: How do you then deal with the system over time? Should privileges once awarded be permanent? If so, at what point should the thresholds which filled the quota from the last point be set? Or should they constantly roll up, meaning, the number of people with particular privileges remains tied a percentage of total users, but who those people are may change?
How to deal with the issue of a "stale pantheon", whereby users can accumulate high rep by virtue of being long term but not necessarily active?
Keep in mind again that part of what makes things problematic for us is an unusually low participation rate in terms of voting; the last point would not be such a big deal otherwise (meaning, again, the system already works as is most places). Part of what we have to do is justify why this is the the nature of our peculiar beast, and something that is unlikely to change, but should be acknowledged and adapted for because there is some reasonable explanation for it.
1. That's not exactly an explanation of that but contains a lot of discussion about it, including, unfortunately, a reference to the "strong support" for raising privilege levels as part of the process.