The broad answer to this, from my perspective, is that both science fiction and history ask the same question about what it means to be human; the difference is that one looks forward and the other looks backward to find the answer. But there are some finer points beneath this broad one. So let's see if I can outline what they are without writing a book's worth of rambles...
~Many Native American cosmologies interpret time as cyclical rather than linear. The example is clear when comparing, say, the Mayan and Aztec calendars, which are round and reused each year, to the square Western calendars, which follow dates in a line from beginning to end and then are useless for the following year. The patterns many Amerindian traditions identify in human history and even the natural life of the universe remind me of some of the best examples of science fiction (Walter Miller's A Canticle for Leibowitz, for example, and Connie Willis's The Doomsday Book), which likewise look for repeating patterns, cycles, and repetitions in the human experience and the life of the galaxy.
~Much of Native American history, and even art and culture and policy today, is preoccupied with and traceable to the initial question -- and problem -- of first contact. Two events that I personally am still trying to wrap my mind around, the Columbian Encounter of 1492 and the U.S. "Indian Removal" of the mid-19th century (think "Trail of Tears" thanks to my Cherokee-centrism), are bound up in the idea of what happens when a group meets the Other. It's not surprising, I think, that science fiction as a genre repeatedly tackles this theme and draws extended metaphors, both explicit and implicit, of the collision of European and American cultures. In fact, I often turn to science fiction (Ray Bradbury's The Martian Chronicles and Mary Doria Russell's The Sparrow, for instance, among others) for added insight into 1492 and its aftermath. The genre also allows us to image what lessons, if any, we have gleaned from past first contacts to apply to future ones.
~Like so much in my life, the heart of this issue comes back for me to J.R.R. Tolkien's essay "On Fairy-Stories." Tolkien's argument -- that it is through fairy-tales and sub-creation that we can tell stories that are True with a big-T kind of Truth -- resonates with me, and I see examples of this over and over again in Amerindian myth, traditions, and contemporary self-expression, in languages rich in symbolism and metaphor, in dream and vision-based stories, in the content of much indigenous art and music and poetry. Telling the facts does not necessarily guarantee that you are telling the truth. Sometimes the most complex, meaningful, and difficult truths can best be communicated through beautiful, well-crafted, conscious fictions. Like Cazaril in Lois McMaster Bujold's The Curse of Chalion, to use a genre example, we may have to search beyond our normal narrative vocabulary for a new medium to express ideas that are too big, too overwhelming for traditional "what, when, why, where, and how" reporting. Certainly I have found that the case in my own work. Some aspects of what I study simply cannot be contained, at least by me, in a straight recounting of dates, names, and statistics.
It may be the case that the post-Scientific Revolution West, the same culture that mistakenly linked the fantasy genre with childhood in a sad "accident of history," is not as well equipped on the whole for thinking in the imaginative terms Tolkien described. At the same time, parts of Native America were and are not similarly handicapped. Science fiction and fantasy authors today, like J.R.R. Tolkien, would be accused by the early C.S. Lewises of the world of "breathing lies through silver" because they write of non-factual elves and dwarves and starships and wormholes, when in fact these authors are sometimes seeking and communicating what is True. That distinction between knowing facts and understanding Truth -- and the warning inherent in it -- is humbling for any student of history!
It seems like I've rambled despite my attempts not to do so, and made some truly alarming overgeneralizations in the process. Ah, well. My point was that I do see areas where the two studies intersect in a powerful way.
And did you notice I never once mentioned Chakotay? You see, I do have some self-restraint left.
I will close with my quotes for the day, two somewhat linked excerpts:
"... our whole nature at its best and least corrupted, its gentlest and most humane, is still soaked with the sense of 'exile.'"
from J.R.R. Tolkien, letter to Christopher Tolkien
"Down New Mexico way
Something about the open road
I knew that he was
Looking for some Indian blood and
Find a little in you, find a little in me
We may be on this road but
We're just impostors in this country, you know..."
from "A Sorta Fairytale," Tori Amos