Following are my ideas on Time Gates, the main time travel system in Chrono Trigger. I've included solutions for every problem I can think of, which mainly goes to show just how limited my imagination is. :) Shred, edit, and comment as desired.
Time Gates are simple ways of traveling in time. Each gate is effectively a 'hole' in the timestream, existing in the same place but in two different times. A person with the proper equipment and mindset can locate and enter Time Gates, moving no distance in space but hundreds or thousands of years in time.
Fortunately, not everyone can use Time Gates. If they could, history would be replete with instances of strange appearances, disappearances, paradoxical occurrences, and general trouble. Time Gates only work for people who possess special objects, such as Gate Keys. For a person who lacks a Gate Key, a Time Gate is nothing more than a strange, multicolored sphere.
When people enter a Time Gate, they enter a state of 'Null Time'. A person in Null Time is effectively outside reality, and cannot touch or be touched by anything. Null Time appears to be a strange landscape of undulating wave energy, speeding by a time traveler at an incredibly fast rate. Although no actual time passes in Null Time, a person who has entered this state will always have a few seconds of memories of the event.
All Time Gates are centered around a Nexus - a being or group with an exceptionally strong will, capable of piercing time. When a Nexus creates a Time Gate, he or she remembers a pivotal event in his or her life, with an intensity that creates a Time Gate back to that era. The Nexus for almost all the Gates in the Chrono Trigger e-game was the Lavos Entity; its memories created Gates that allowed Crono and his companions to transcend time. After the death of the Lavos Entity, Crono and his companions jointly assumed the position of Nexus for the Lavos Gates, keeping them functioning.
For a brief time, Lucca became the Nexus for a single Gate, one leading back to a pivotal time in her own life. Using this Gate, Lucca had the opportinity to go back in time and change history.
The very concept of time travel allows for apparent paradox - a person goes back in time and prevents a disaster that would otherwise cause major destruction. Time has now been changed and the disaster never happened, so how would anybody know about the disaster in order to change it? However, the nature of Nexuses and Time Gates provides a solution. Each Nexus has an exceptionally strong mind and will - the requirement to be a Nexus - and is capable of comprehending *both* possible outcomes of a pivotal event. Because of this, a Nexus *is* capable of understanding a disaster that might have occurred, and influencing others to prevent it.
Time machines, like Epoch in Chrono Trigger, can be constructed. These machines are capable of forming Time Gates at any place, and travveling to other times. However, no machine can be a nexus on its own. Each machine must be attuned to an existing Nexus - as Epoch was to the Lavos Entity - and the machine can only form Time Gates to eras that the Nexus has existing Time Gates to. This is why Epoch could travel in time to 600 AD and 1000 AD, but not to 800 AD. Since Epoch was attuned to the Lavos Entity, and not Lucca, it could not travel to 990 AD, either.
All Time Gates look alike when not in use - a black sphere, about a foot across, floating in thin air. However, activated Time Gates are different colors, according to the personality and nature of the Nexus. The standard Time Gate in Chrono Trigger was blue and purple when activated, its colors were blue and purple - the colors of teh Lavos Entity. When Lucca entered her Time Gate, its colors were gold and red.
Rob decides to start a Chrono Trigger campaign. (Hey, rob, if you *do* do this, can I play?) He decides taht the campaign will start at the End of Time - the players have been brought there by Gaspar, the Guru of Time, who needs champions to face off against an Ultimate Evil. Rob doesn't want to use the existing Chrono Trigger eras, so he decides that something has destroyed the existing Gates. In order to travel in time, the players will have to seek out and find other Nexuses. The first - Gaspar.
Rob's 'Gaspar' series of Gates will span three eras. The first age is the End of Time, an obvious starting point, and convenient for the characters too. Rob decides that tbe second age is sometime around 12000 BC - not contiguous with the 12000 BC Gate in the e-game (that could get the characters into fights with Lavos, or worse, Crono and his friends), but close. For the third age, Rob makes up some background for the Chrono Trigger. This item, Gaspar's masterwork, required many items, including one provided by a time traveler from 4500 AD - the third age
Rob sits down and does some writing on the eras covered by the Gaspar Gates. This includes not only basic worldbook information, but also connections to other ages and information on other Nexuses available in those ages. For example, both Melchior and Balthasar, the other two Gurus, can both be found in 12000 BC. Either of those could serve as Nexuses for other Time Gates.