I saw Ex Machina also. I didn't hate it but I just didn't like it as much as I thought I would. Can't quite explain why.
On Annihilation, they never really gave a good explanation for the all female cast. That didn't bother me though. What I really liked about the movie is how utterly alien whatever it was that thing they were up against was. Machine? Biological? Some kind of Deity? Was the harm it causing malicious or accident? I feel that they were intentionally aiming for something inscrutable which added immensely to the horror aspect.
Υes, I thought the most effective aspect was that you had no idea what caused these things or why it did. Which seems to be what annoyed a lot of the people who were annoyed by it. Also maybe it was badly marketed and they were misled? I don't know.
Some issues I had with it were that:
1) Some performances weren't very good. Particularly that of Gina Rodriguez.
2) Yes, some things didn't make sense. It seems like the best option would be, instead of going straight for the lighthouse, maybe they should have sent teams in just to take a glance at things, and immediately return, just to prepare the ground. Also, if it was easier to access it from the coast, why did they not enter it from the coast? Why were they guarding the perimeter from down there instead of from the balcony (that was probably the most annoying one)? There were a few others too but they were minor. Also, yeah, the science didn't really make sense either, but that's entirely ok. I saw some guy from IMDB complaining about the science, and saying at some other point in the review that you should watch Black Panther instead. Which was just weird.
3) I'm not sure yet if the whole thing about the protagonist's affair was entirely necessary. Maybe it had some importance that I missed (maybe it was connected with the self destruction Ventress talked about?). Idk. But it seemed sort of unnecessary.
4) To me it seemed like it drew a bit too heavily from Arrival, which is an amazing movie (better than this one), but sometimes this felt a little bit too similar.
5) A big chunk of it was pretty predictable, and some revelations felt weak for that reason. Actually some of them didn't even feel like revelations. However it didn't really harm the whole aura of mystery of the film.
6) The CGI ranged from some of the best I've seen, to... shaky at best. A bit of inconsistency there.
So there you have it. These are the main flaws I found. I don't think it's perfect but it's definitely one of the best things I've watched this year. My interpretation is not 100% solid right now, I'll think about it a bit more.