Heavily recycled content
That's been the game from like EP2, people hated all the Mining Base stuff, that we had and nothing else in JP. This game didn't have a lot of actual content outside of glamour forever really.
Near zero collab content compared to JP server
While that sucks, it's not really important, as the promise was just content and dressing up is nice, but that's not really actual content.
Sega withholding important content and/or has no plan to implement for global
We aren't missing any important content, and we are still getting the later updates, like the new challenge mode, and NGS will roll out over in global also, with the better graphics update.
That's the game, they didn't really fix that only in JP. The skill trees were kind of a mistake balance wise.
Toxic/elitist player base
You need to speak with more people, I met tones of really nice people in global. It's why I avoided SHIP2 in global, because of how the english players acted. But I have seen the avoid players pages posted in 2ch about this game. JP players also are capable of malice, just because you can't understand it, or see it, doesn't mean it doesn't exist.
Hackers/Bots and RMTs
JP had hackers first, and they also had exploits. They did take care of the public bots that would post messages, but it's still a thing.
Dramatic loss of player base across all servers
The game has been out for years in Japan, it's going to lose players, and it's also near the end of life. With NGS coming out, we'll see a increase for both JP and Global, due to being a new game.
They really are close to each other outside, a few missing fashion items. I hate the localization job Global has gotten with the crappy weapon descriptions. JP version of this game isn't really a golden mine, and I like how less fluff global has when it comes to progression, compared to JP.