While Swift Swim Palkia may seem to be a huge threat due to its blistering speed and great STAB Water Spout/Hydro Pump, it is countered fairly easily by Prankster Spore, Sturdy Shedinja and Imposter Blissey; all of whom are quite common in the tier. The speed boost from Swift Swim is not as significant as you might think due to how common priority is in BH (which is also why Speed Boost is fairly rare), and Swift Swim is less useful than abilities such as Magic Bounce and Contrary.
To get past Giratina, you really just need strong super-effective moves. Due to the prominence of Prankster + Copycat + Whirlwind, Magic Bounce is also recommended to deal with such variants, as well as variants that use spore. (Verbatim posted a Latias set earlier in the thread which would work quite well, though Latios takes a lot of damage from Dragon Tail.)
Originally Posted by Fat verbatim
Latios @ Soul Dew
-Spacial Rend [62.02 - 73.16% vs Giratina when unboosted]
While this set requires slightly more set up than Contrary to use (it's worth noting that Soul Dew Latios can already hit incredibly hard off the bat if need be), it does alleviate status concerns as well as offering access to both of Latios's STABs. While it is relatively minor, one should not forget that Aura Sphere backed by Soul Dew allows Latios to take care of Moody pokemon in the event that your Blissey is out of commision/being saved for latter.
To deal with Imposter Blissey, you just need to make sure that all of your sweepers can be countered by another pokemon on your team. Sturdy Shedinja is an easy way of doing this, as it walls any sweeper without Mold Breaker or a status move. Shedinja also has nothing to fear from Blissey, as Blissey does not copy Shedinja's unique HP stat.
Giving your lead Magic Coat will help in dealing with Deoxys-S, as it will prevent it from setting up hazards or putting your lead to sleep (Magic Bounce also works, but it is negated by variants that have Mold Breaker).
If you have not already, I recommend reading the Introduction to "Balanced" Hackmons
article in the Smog. It gives some information on the tier's threats, as well as how to counter them.