Sorry "Surprise", but LOTR was very original for its time and influenced a whole generation of writers including the writers from Squaresoft. Probably not original now, mostly because everyone has ripped the storyline from it in some shape or fashion (a group of heroes travel to distant lands filled with obstacles with the ultimate goal of destroying a single great and powerful evil to save the world). Plus, although I havent played Chronotriger, Kane has a point, a time-travel storyline of discovering a destructive event outside of the present that could destroy the world, erase, or change time has been done plenty of times and is very cliche, while LOTR was extremely fresh for its time. Adding a manga flair and littering the story with fluff like sub-plots doesn't make a story anymore fresh or original, just hides the fact that it isn't.
Actually, the fluff in RPGs is my biggest pet-peeve, who cares if Main character #7 has a brother who is still alive and now wants to kill him? Must we go find him if it has no relevance ot the core conflict? Who cares M. Character # 5 might be his secret father, who is collaberating with Irrelevent Villain #3 and Love interest#2? (who will later be revealed to belong to a guild of psychics called "The Minds", in irrelevant-dumb-plot-twist #9) Apparently gamers do, since these distractions from the plot are in the majority of RPGs, but you don't have to play an RPG to get this kind of entertainment, just go watch a soap opera. In a 2-3 hour movie, try to stick this kind of fluff that constantly steers away from the main plot, and I gurantee you you will bore most Western audiences out of their mind. Some will stay and enjoy the movie, most likely people who like soap operas, and the rest will leave. (George R.R Martin's "A Song of Fire and Ice" had a lot of sub-plots, but they all revolved around the central conflict, the game of thrones, which is what made the story work and made it somewhat interesting.)
Tolkiens influence was not just inside the realm of fantasy eithier. Issac Asimov, who influenced directly or indirectly almost every Sci-Fi author after him, also labeled Tolkien as one of his big influences. Asimov learned from Tolkien that in order to create a new world and make it come alive you must create a detailed history that goes along with it. I am not a diehard fan of Tolkien,but I do enjoy his work, and achnowledge his impact on modern writing.
And honestly, I thought the plot of Chrono Trigger sounded pretty corny, like something out of a 30s or 40s pulp-magazine. Change those numbers around and you get a plot thats been done much more then once. Perhaps its execution is much better, hence its appeal, but original it is not. It got old after "A Wrinkle in Time", and the hundruds of pulp-adventures in the 40s that butchered the concept to death.
Out of curiousity, do you mean the world ends when evil now resides there? Because if the world will end 999 years after their time, how could they travel to the year 2300AD after the world ended? The world would be gone.