Disclaimer: I played through the Saki battle in v13 and with a new save file I am just about to enter Axis High in v13.5 so forgive me if my questions are answered or my theories debunked later on.
Team Xen as an organization, lets talk about them. On the surface level, they seem to be a para-military organization. A few issues I have with that though. At the start of the game, they seem to be seen as a nuisance but mostly harmless. We know that is not true and they have a vast membership as well as a large amount of military hardware. Even if they got all their battleships, trucks, flying suits, and other equipment from a different region you would still assume that news of somebody buying up a small armies worth of tech would get around. They also seem to have a huge membership, I know there are some repeat trainers and I plan on doing another playthrough and recording the names off all the Xen members that you fight, but having a group with so many members should also be hard to hide. Even if they are "mostly harmless", if they number in the hundreds, they would be a major power in the region. We are also told that Team Xen existed in the past under a different leader.
The tech that they have access to is also a big question mark. They can put Ren's consciousness into a cyborg body, the Deathwings have powered flying suits, Madam X is capable of superhuman speed and strength however we don't know if that is because of her suit or her personal abilities. We don't see that kind of tech used by anyone else in the modern timeline. During the Neo-Geran sidequests we see a Deathwing get his wing damaged and it repair itself later, however it seems to take a physical toll on him. We also hear Madam X say "If it wasn't for this damn suit..." which I take to mean that the suit is not an optional thing for her and also it is limiting her abilities somewhat.
All of the members that we really talk to seem to have some personal goal that their membership in Team Xen will help them with. From healing a sick family member to downright cold blooded revenge, they all seem to want something that they feel like they can't do themselves. Team Xen is also a one-way street. Once you are a member, you don't leave without being erased.
Being erased is another oddity. If you wanted to control someone, a good old-fashioned way is to implant a little bomb in their neck to pop the head off if they get out of line, but that is not what Xen does. I can't help but assume it has something to do with the green gem they all carry. The way they are erased reminds me of what happened to Aelita in the past with the Vivian situation, making me thing that the green gems act like a timegear amulet.
My theory is that Team Xen is made up mostly of people from previous versions of the world or from different timelines looking to change something that happened to them in the past. The gems act as artificial protection from being erased like they should have been in the last reset of the world, so deactivating the gems lets the world correct itself. Madam X took her name from the team, not naming the team after herself.
This doesn't explain how Team Xen was able to acquire so much tech and hardware. If they brought things like their Battleships from the previous reset, then they should also have a time-protection device, but if so why wasn't it just remotely disabled when Neved's battleship was stolen, dropping all the passengers off into the middle of the ocean? The Deathwings could have been outfitted with their suits in the previous timeline and brought them with them, the same for Madam X and her suit. And lets not forget our good friends the Silver Surfer and Mysterio, they are using equipment and tech that far surpasses the level of what is available in the modern timeline as well.
What do you think?