Vaporeon and Lapras are both useful in countering the rain archetype, since they both get Water Absorb as an ability. However, Freeze Dry is this really cool move that does super-effective damage against Water-type Pokémon. And Lapras gets access to it! So that made my decision easier.
After having chosen Lapras, however, I was really unsure of whether to go for Shell Armour or Water Absorb as my ability. I thought having Water Absorb could prove a bit superfluous, as Lapras already has resistances to water and ice moves (both common on Rain team Pokémon, as we all know).
I needed to take my current team into account when deciding on my ability. There wasn't a lot of bulk on it, and having an out to heal back HP was more tempting than never being hit with crits. So I started with Water Absorb and worked my way on from there.