Let's see.
Well, generally-speaking, clichés and trophes I "hate", but unfortunately can definitely imagine them being present in Andromeda, because BioWare:
º A " chosen one " protagonist. I sort of hate it because it's extremely overused... but it seems to work most of the time anyway. It's fast-food story telling.
º A " misunderstood " enemy / antagonist. I hate it usually because I can't tell if the author(s) were simply lazy and couldn't make the actual enemy's intentions clear (at any given point in the story), or if they really wanted us (the audience) to actually misunderstand (which then becomes sort of a brilliantly-written and planned out story... if it works). The problem, indeed - and to repeat myself - is that ultimately nothing is clear (I.E. I have to "guess").
º Discovering ruins / remnants of long-gone ancient civilization(s). It's only useful and meaningful if it actually plays part of the story at hand that's currently unfolding, especially if I don't have to wait an extra or two installments in a series to finally see what all those ruins and impossible-to-currently-understand artifacts actually do. If you want us to explore planets in a new galaxy that we know absolutely nothing about - in which it is guaranteed that an untold number of civilizations had their time and then went poof at some point - only to eventually and inevitably find Prothean-style ruins scattered around... then PLEASE give us actual information about said "gone" civilization that we're discovering things about BEFORE having to wait for the final "big reveal" that we always seem to have to wait for until the sequel, or the sequel of the sequel comes out 3 to 6 years later. I do NOT want to see my teammates going nuts over some egg-shaped alien 'device' that I found in some unknown ruins and brought back to my ship only to still have the thing levitating uselessly in some containment room when it played zero freakin' role whatsoever and generated a maximum of three conversations by the time the credits roll on screen.
º Having to wait until the final mission, or the one just before it, before being able to bang your Love Interest. Ok, seriously. Please, don't do it? I'm asking gently. Also, it's not exactly just literal, but also figurative. I'm not just referring to a " sex / love " scene. I'm referring to either us (protagonist) or the LI to reveal his/her feelings for the other. It could just be a short speech or something. Or, of course, the actual love scene(s) (well there's usually just one, and not always for every available LI anyway). It's a damn lazy and senseless cliché that the blue chick is going to wait for the moment when she realizes " OH ****!... that mission sounds REALLY serious, like... more serious than the twenty we did before it in the past month. I mean this time the bad guy will be there IN PERSON. Damn, better go see that girl/man I've been lusting for all that time to see if something can happen 'coz HOT DAMN I wouldn't want to die before being able to see his/her bombchicapowow! ".
º Leaving the ending and the main story arc (by the time the credits roll) with " open to interpretation " routes about what in the bloody great heck actually happened. I know there's going to be disagreements because apparently there's people who would actually eat conjecture if they could. I, for one, usually absolutely loathe being forced to interprete story or characters-specifically elements. Now, I said 'usually', because in very rare cases it can work to some degree, but only when done with control and moderation by the writer(s) (it also depends on the context at hand). I still generally just hate it though. I see that as a form of complete laziness in writing, but most importantly in IMAGINING. If you're a writer, and you create a context / condition in which one or more characters end up trapped, or blocked (just examples) and you just STOP the development of that scene, then we have to guess "Sooooooo... hummmm... wait so... did the guy get crushed by the machine or... ?" Did he actually manage to climb up to escape? And if he did... how did he get rid of the three guards above making sure nothing would go wrong? And wouldn't the guards just fire at him anyway if he attempted anything, ensuring his doom down there? * facepalm * Seriously, if you want to be a writer, and a story-teller, then WRITE me a story and TELL me what's happening! My 'job' is NOT to sit down and continue your work on my own dammit! I'm here to enjoy reading a story, not just breaking eye contact from the page / scene I was immersed in only to end up staring silently at the wall confused by what I'm supposed to think on my own to make sense of what you couldn't think of yourself.
The kind of context, or obvious situations I can sort of tolerate interpretation (doesn't mean I actually like it though) is usually when I KNOW that something else about previously-incompleted scene / conversation is going to happen (or be "revealed") either within the next pages / scenes / hours (of game-play) or, in the worst case scenario, in the next book / chapter / game sequel. But if that's the case then it MUST have been made clear in the situation itself (or perhaps a bit later on) that we WILL see or hear of it again. Don't just leave us in the complete void and unknown... THAT is when it not only makes my blood boil but it feels cheap.
Anyways... that's what I can think of for now (and, yeah, no... I don't want to see any such clichés in Andromeda, but yes I believe at least one of them will make it).