Mysteries of the Sith makes the odd choice of changing the viewpoint character after the first four missions. I get that they might want to set up a "passing the torch" situation where a series that had previously been about Kyle Katarn is now going to focus on Mara Jade, but why that needed to be more than a single starting level, I can't say.
I'm not sure how I feel about this Mara Jade character. She's got "attitude," which tends to be entertaining, but is so "90s" it's almost embarrassing. I wouldn't ship her with Luke Skywalker, but she seems like an interesting enough character to stand on her own. I'd say it's more or less a lateral move from Kyle Katarn.
I've got no idea about what's going on in the game's plot, however. I think Mara Jade is just running various errands for the new Republic. In my latest mission, I have to protect a holocron from space pirates, which gets my narrative-detection senses tingling. I have a feeling that there's going to be some shocking secret revealed in the course of defending this ancient artifact, but that's only because the game is long overdue for something significant to happen.
It doesn't really matter, though. I decided that I was not particularly interested in the Kyle Katarn saga somewhere around halfway through Dark Forces II. It's a functional enough video game plot, but that just means it's an excuse for running around a series of 3D maps blasting enemies and hitting switches. So far Mysteries of the Sith is doing well on that front. The levels are a bit more open-ended than Dark Forces II, but not quite as confusingly laid out as the original Dark Forces. They also use their verticality more than those from the first two games in the series, so I'm guessing that by1998 game developers were pretty comfortable with 3D.
I think I'm going to have a pretty easy time finishing this game, though I'm predicting that it will come in at about 12 hours for my first playthrough. It's possible that there might be an impassible difficulty spike before then (I found myself reloading the prison level way too many times thanks to the way it stranded me without weapons), but if that happens I'm likely to just cheat my way through, so there's pretty much nothing that's going to stop me from getting to the end.