That actually sounds like an awesome game, I'll have to try it when I get some free time.
A book I read that deals with time travel and the paradoxes that come with it is "Up The Line" by Robert Silverberg, written in the late 60's. Being from the 60's, it has a lot of hippie free love, and drug usage influences, but overall a good story. Silverberg covers a heck of a lot of paradoxes and rules about time travel that I hadn't really even considered at the time before I read the book:
"Accumulation Paradox": The book uses the example of Christ's Crucifixion, and you avoided it in your game by making the player invisible... If a person visits the same event in time many times, would every version of that person already be there? or does it accumulate after each trip. In other words: if Christ's Crucifixion was a "hot spot" for time tourists, and they kept going back there over and over again, eventually there would be hundreds of thousands of people all standing around watching the event, though history has not recorded such a mass of people being there at the time. It's explained better in the book
"Transit Displacement Paradox": This was used in the book as a sort of loophole to prevent the main character from instantly being altered by his actions. This just simply states that when a time traveler is not in his "present time" he is not in his own "time matrix" and is protected by a "temporal bubble" that conserves his history, despite how his new present has now changed.
"Discontinuity Paradox": Happens when you bump into someone that left from a future time than you did, and thus knows more about you and your future than you do. This can also work in reverse when you run into someone that is from a past present, with whom you haven't technically met yet.
"Duplication Paradox": This one's a doosey
It happens when you interrupt the past and thus create a duplicate of yourself. An example of this would be to stop yourself from traveling through time. Since you didn't travel through time, the version of you that stopped you from time traveling shouldn't exist, but using the "Transit Displacement Paradox," there is no paradox and you don't vanish until you return to your present time.
"Final Paradox": The paradox that in changing history that will prevent time travel from being invented.
There's some others but I can't recall them at this time.
I have made a prototype "Paradox Simulator" but as of this moment, it is only in a beta stage. It runs in a DOS window, and is a bit clunky, but I one day hope to do it in either 3D or at the very least in 2D. Basically all this does is allow you to move a small circle in an enclosed rectangle, and travel to any time you want. "Time" is indicated by integer numbers. So you start off at 0 (zero) and can go to any number above that... 234, 5, 42, etc. and back again. Give it a try. You'll get a sense of deja vu from playing it once you start noticing that there are 20 different versions of yourself in the same space at once. And I haven't really programmed it to do anything when you bump into your past self other than destroy the universe
Make sure it's in its own folder, because it'll create about 20 text files used to record player movement and it's a pain to have to find them in a bunch of other files if you didn't put the program into its own folder.
http://formatted.homestead.com/files/paradox.zip
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but the idea is kinda weird also I mean I saw something on TV about Time travel like think of it this way if you went back in time to your first day at school and then left wouldn't you keep going back in time over and over again because the old you the first one that went back in time. 
but then the you going to school that the future you went to see grow up and wouldn't he back in time just like the first one. 
and what was with the guy in shadow of destiny did he seem like the devil or was it just me?
I'm too tired to play to get the other ... blah like 10 endings. 
) because I've been on it for 11 or so hours and I'm not even on disc 2 yet 
it is similar to Myst
