I've been reading Mass Effect fanfiction and thinking again about all the missed opportunities of the Tomb Raider (2013) game.
Had some trivial thoughts about the Harry Potter universe as well. Main one; the story is hermetic. It is about magic versus magic. Neither the magic system nor the entire Magical World as presented are ever intended to interact with anything outside of magic and the magical world. Thus to my mind cross-overs and most fixfics are non-starters; magic is an out-of-context problem to any other setting, and the muggle world (be it our world or the world of Darth Vader) is an out-of-context problem for the magic world. It makes as much sense as asking whether a Checker can put a King in check, or how many spaces a domino advances in Monopoly.
The other is that the magical world is Britain between the wars. They lost so many in the first Wizarding War against Voldemort, they simply can't deal with the threat of a second one. They don't want to believe it possible, and they can't bring themselves to commit to planning against it, they don't even want to talk about it. Thus the ineffectual and even counter-productive actions by so many of the adult characters, and the willful ignorance they impose on the young characters.
And that led to the first thought; perhaps the best way to break the pattern of what happens to Lara Croft on Yamatai is to pick a character who comes to their interactions with the world from an entirely different context. Say, Sherlock Holmes. First Bunny here; Holmes and Watson on Yamatai, with the Endurance expedition taking place in the late Victorian age. A lot more deduction, a lot less shooting (well, unless you cast the Robert Downey version).
Flipping that, though, since the story of Lara on Yamatai is about growing from a scared kid into a survivor...switch up and put Lara in Shepard's shoes. In the Mindoir origin. Given the way the events of Yamatai unfolded, I'd say it would be a bad day to be a Batarian.
(There's another Bunny lurking here; given that the archaeology of Liara T'soni is what gives the first good clues to the nature of the Reapers, some of the tools used to defeat Sovereign, and in one of the outcomes of the third game leads to the only really decent resolution, one could make an argument that an adventure archaeologist makes as much a fitting protagonist for the story as does the universe's most persuasive soldier-hero since Darth Revan.)
From a completely un-quantified survey of Fanfiction.net, about a third of the Lara Croft stories are set in the 2013 reboot continuity (almost another third are in the original continuity, post Angel of Darkness, and include Kurtis as a character), and of those the majority are post-Yamatai and of that number the majority are Lara/Sam fics. There's also a sizable contingent of Amanda fics, and just enough of a sampling to be statistically significant of Lara/Natla fics.
Of the Harry Potter fics that have attracted my eye, most have turned out to be fixfics. Either crossovers or introduction of out-of-context elements like dragonriders or unexplained new powers or just plain Harry-gets-a-clue, they almost inevitably reveal the rest of the magical world as a bunch of dopes. To my mind, it never really works (as much fun as a snarky bit of "take that!" can be).
What few Mass Effect fics I've looked show the following trends; generally through all three games or set post, inevitably femshep (aka Commander Shepard is female), and she most often romances Garrus (I agree -- I was happy enough to leave Kaiden on Virmire.)
The vast majority of SG1 fics are Jack/Sam. But there's a statistically significant trend for builder fics, in which the Stargate Program is managed differently, with different methods, gear, etc. The best of which so far is one set in the late 40's, with an Ernest Littlefield who remembers to take a radio along.
And mostly unrelated: the title music to Tomb Raider: Angel of Darkness (which opens with Lara's old mentor Werner von Croy getting killed in Paris) reprises the main theme from Tomb Raider: Revelations (in which that character was strongly featured.) So I'll definitely see if I can work a reference to that theme in the Tomb Raider: Legacy title track I'm tinkering up!
(Which will be multi-tracked with a little pennywhistle and violin from your's truly. The violin is I'm afraid going to have to track itself into string sections, though. I am years from being able to do a soulful solo on that instrument.)