Increasing mob difficulty in Dynamis is just one of many things SE could do to prevent this issue. I can think of a number of additional ways that SE could help the situation... whether they would do any of them or not remains to be seen.
1) They could level cap Dynamis to 75. I don't see them doing this, given that if they didn't do it already, they aren't going to, plus with the recent removal of level caps for other things, I can't see then adding new ones.
2) They could instance Dynamis (not bloody likely), or in lieu of that, at least implement multiple copies of existing zones. For example, say there were FOUR trail markings in Xarca that all lead to identical Dynamis Xarcabard zones. You don't have an unlimited number like an instance would support, but at least you have a limited number of multiples available, plus that might be far easier to implement (though I'm no MMO programmer, so idk).
3) They could restrict entry to once a week instead of every 3 days. Not one of the better solutions, but since most shells go twice a week, this would be a fast way to double capacity with minimal effort. Though prime times would still be an issue.
4) They could introduce another event that drops ancient currency in the quantities that Dynamis does. Since most Relic armor is not exactly awesome, and with all the new content and the hint of a third high-level Artifact set, ancient currency for relic upgrades is one of the primary driving factors for keeping Dynamis popular. If there was an alternate way to acquire currency, that might take a good bit of the load off of Dynamis zones.
5) Lower the entry fee for CoP zones (or increase currency drop rates in CoP zones). These zones are under utilized at the moment because they aren't nearly as profitable as the original zones, and they are more difficult to clear. The difficult of killing the bosses of the zones (that effing Malboro in Valk comes to mind) should resolve itself as the level cap goes up, provided they don't also cap Dynamis to 75 (in which case, reducing the difficulty might be an option). So if they could make those zones more profitable, I think they could become more viable alternatives to the original zones than they are currently, and distribute some of the load better.
6) Require a minimum number of people to enter a zone. Admittedly, I'm grasping at straws by this point, and I'm not sure how this could be implemented to not end up causing more problems than it solves, but if there was a way to prevent group of 6 people from claiming a zone for 3.5 hours, it might help.
I'm sure there are other ideas I'm not thinking of, but the point is just that there's lots of things SE could do, if they cared enough to try.