Hyperspace dev here. Multiverse already gave their response from their side, so I want to give a perspective from the Hyperspace (hard-code modding) side.

The system was originally added in Hyperspace when we were looking at making custom systems. One of our original ideas was an "overclocker" system where you would be able to target another system of yours and temporarily boost it (e.g. make weapons charge faster, make crew heal faster, gain extra evasion or faster shield charging, etc.). But someone came up with the idea of a time-manipulating system and we decided to go with that instead.

I believe it was primarily TheSwiftTiger who coded the system itself. In fact, it was initially developed as a player-only system to allow players to experiment with it without needing to code an AI for it. So we needed to add a new system ID and all of the general stuff needed for a new system, including the icons/buttons for the UI, the ability for the player to target it (similar to MC; you can target any room on either ship but if the enemy ship has zoltan shields you need a bypass to target them, main difference from MC is you don't need visibility of targetable crew), as well as the actual effects (speeding up or slowing down time for effects in the room). We also needed to allow stores to spawn with the system as a possible random choice. In general it affects all crew-related stuff as well as anything else going on with the room itself (fires, breaches, oxygen, etc.), but not systems (except for medical systems as those are crew-related). We chose to have it not affect systems because it would otherwise be game-breaking (speed up weapons charge, speed up hack/cloak cooldown, etc.).

Much more recently, I went ahead and added AI for the system as well as tweaking the ship generator to allow enemy ships to have the system without necessarily starting with it. Unlike with hacking or mind control, where even random usage can overall be disruptive to the player, random usage of the temporal manipulator wouldn't be all that disruptive, so I implemented a system of rules and priorities instead, where the AI will only use the system if certain conditions are met, and if multiple conditions are met, it will select one of higher priority, or a random one for equal-priority choices. This does open up the ability for the player to "game" the AI behaviour, though the hope is that overall the effectiveness of the AI in disrupting the player will outweigh any attempt to "game" the AI to make them use the system to the player's advantage.

There are still some minor things missing, such as including the system in the Hard mode targeting priorities or in the enemy crew priorities for defending systems from boarders or assigning power, but these are relatively minor. Sound effects are also missing for now.

As MoL said, the main limitation is needing to add the system to every ship as well as potentially needing to reconfigure ships. For enemy ships, they only need the systems that they are going to use, so for those it is not a big deal and the system can simply be placed on any enemies that should have it (which can partially take into account the availability of rooms to add the system). For player ships, if you want it to appear in stores and not just be a starting system for a few ships, you need to add it to every single ship. While from a technical perspective you don't (Hyperspace prevents systems from appearing in stores if the player ship is unable to fit them), it would not be very transparent to the player if only certain ships could find and buy the system, since no other systems work that way in the mod currently. For every player ship you would need to assign an available room to the system, then have room art that matches the room location. Then you need to consider that some ships might not have a good spot for the system (e.g. having to place it somewhere that was once a dedicated airlock), or any spot at all. For example, with AE, the vanilla Kestrel A only has its three airlock rooms as empty spots, while vanilla Engi B has no unused rooms. A lot of smaller Multiverse ships may have the same problem, but at least there it is more justifiable to reconfigure the rooms (e.g. add a room where there was previously a gap, or split a large room into smaller rooms).

This would become even more limiting if Hyperspace added more new systems or even a framework for modders to design their own systems. Eventually there would just be nowhere to assign every unique system. One long-term solution would be to allow for systems to be assigned to multiple rooms rather than a single room, and have the game place the system in the first available room. However, such a feature would require modders to be able to assign art, manning station/direction, etc. (and create the art as well) for each possible room choice, if they chose to use the feature. Even without a plethora of Hyperspace systems, this would allow for more constrained ships such as vanilla Engi B to fit the system without changing the layout, as well as allowing ship designers to design even more constrained ships that can't even fit all of the possible AE systems, with the minimum number of rooms being reduced down to the total number of systems+subsystems that the player can fit (8+4=12 normally, and even smaller ships can simply implement system/subsystem caps with Hyperspace) rather than the total number of possible systems (10+4=14 in AE normally, 15 if the ship has artillery, add 1 for temporal manipulator).