Yea, Cresselia is certainly one tough duck to take out for rain teams. Thankfully, Rain neuters Cresselia's Moonlight, so it can't wall the team forever (unless it has Sunny Day). However it certainly cannot easily switch safely into Kabutops' LO Waterfall or even worse Ludicolo's Hydro Pump, so it's a Rain check at best. Slowking basically does a good job checking rain than Cresselia. If Omastar gets a Shell Smash in the rain, then forget it (might be cool to try Lum Berrry on it to remove paralysis)!
If you do find yourself having trouble against Cresselia, SubDD Crawdaunt is certainly an interesting choice for rain; it can set up Substitute to block T-Wave, set up DD, and start wrecking everything in the downpour! Rain-powered Adaptability Waterfall and super-effective Adaptability Crunch FTW!~