It was very late when I got to that decision and I didn't spend much time on it (the game kept hitting us over the head with how in love he is with Claire, over and over), I went with Claire. She seems like a drug to MC/Blake. But your point about the two years is hard to ignore, if I'm playing the more moral version of him, also considering Beth may have a rougher time of the journey than the L's, so it would be kinder to wake her up nearer the destination.
Maybe we'll get a chance to rescue them from the other ship. I do wonder why Wildman went with so many soft decisions (which neighbour, which strategy with the young religious girl, etc.) and then a few really hard ones (Nemy v. Daphne, and B.C. v L.L.) where it's not just minor temporary changes, but massive permanent branches in the story and cast. I imagine it's going to be a crazy amount more work that way.
I made the same Lexi/Lauren choice. Lauren has already initiated a regular threesome event with MC so she's going to be fine with the harem. Also she invented Paige so is the best suited to help MC and Paige navigate anything going on with the implant and how to expand Paige (maybe even giving her a body?). Beth doesn't bring anything to the table other than perpetual guilt for MC, and Claire even less other than distracting MC from spending time with the other girls on the ship. Plus Lexi is goddamn Lexi and deserves to get woken up no matter who she's paired with.
This actually brings up another point I considered in this Major Choice. Namely, how Claire and Lexi will likely react in 2+ years if they aren't woken up.
Claire already has an established relationship with MC and feels pretty secure about it. If she wakes up 2 years from now and finds out MC has a harem of beautiful women he's been with for 2 years, some of which might be pregnant or have kids, I can legit almost see her giving MC a high five and saying, "Nice job! Guess I have some introductions and making up for lost time to do, huh?"
Lexi by comparison just started her relationship with MC after crushing on him for a very long time. She's still insecure about it and feeling overlooked by MC. If
she wakes up 2 years from now to the same circumstances, I imagine it'd be much more of a shock. Even if she's okay with MC being with other women, she'd likely feel even
more behind.
So waking up Lexi now when your harem relationships are pretty new puts her in a much more equal place comparatively and gives your relationship with her opportunity to grow alongside all the other new ones. I actually think that if you could ask Claire, she might tell MC to pick Lexi instead. From what I remember, she encourages MC to explore that relationship possibility with Lexi. If it makes no big difference to Claire personally whether she's woken up now or later, she might prioritize her daughter's happiness.