How can your main character "hide" the technology? I mean if mankind was at that point in their evolution to discover how to utilize the 4th dimension then don't you think that they'd "rediscover" it even if the working prototypes were hidden? Instead why not have this discovered dimension usher manking in a new era where they are not bound by Time. I'd love to see a more optimistic view. I know we're not doing too great in this time but who says we won't smarten up one day?

Your story didn't sweep me off my feet but it can be worked into something decent. I mean there aren't that many original stories anymore, you just have to know how to work with what you've got. Don't get discouraged by the mostly negative feedback. Rework it and come back and show us what you've come up with. :)

I think with some serious thought you can make it into a good game, but then, I've seen company's take good concepts and come out with relatively dull games (to me, anyway)

The first thing that came to my mind was that "If they DO fix their 'glitch' why not go back to the time they got stuck with the aliens and rescue themselves in the past, or warn about the glitch before activating the ship" at which point you have to decide whether you create a time paradox or if time traveling only creates alternate dimensions which would mean that the original dimension was still doomed to make the mistake.

Time travel is a hard kind of concept to work around, because time is another barrier for the player. Things happen in chronological order so that in order to get through the blue door, you need the blue keycard. You can't go through the door without first getting that card.

When you have time travel involved, you could technically reverse time for a door to a time when it was opened already, or reverse time for a building to before it was built, or fast forward it until it crumbles from decay.

And It's hard to avoid plotholes when only theoretical concepts are being used, so like I said... it will require ALOT of thought to pull off.

Finally, if someone were to steal your concept, their game and yours would still be so unbelievably different that it wouldn't matter. Your game could be Starcraft to the other persons Warcraft, or pokemon to Digimon, or a flight simulator to Star Wars rogue Squadron...

Why would the aliens want to kill/enslave us rather than absorb our culture into their empire?

Because that's what empires are. A group of autonomous(sp?) states that are ruled over by one leader - the emperor.

And if they thought that the time-ship-thing was interesting, wouldn't that make them want to keep us alive so we can make more cool stuff for them?

Maybe their leader(s) aren't very bright and are going against their people's wishes. That makes the people pissed, so they start doing stuff. Like protesting. Or the human race, being the psychotic mass of instability that it is, misunderstands the intentions of the aliens and attack first, setting off a war that neither side really wants. That would make the plot more interesting, non? The idea of "oh noes the aliens are gonna kill us all" is getting kinda tired, ya know?

Or maybe the main character has the only remaining blueprint/whatever of the time-thingamibob (he somehow manages to get rid of all the alien's data and equipment) and he's being chased by BOTH humans and aliens, who eventually join forces to stop him from destroying/losing the thingy.