BW Zekrom:
+ Good check to Ho-Oh / defensive Kyogre
+ Monstrous Attack stat
+ Dangerous STAB combination
+ Reasonable bulk
- Choice Scarf not great when there are better users of the item (Genesect comes to mind)
- Subpar Speed tier leaves it vulnerable to revenge killing by the omnipresent Palkia / not-uncommon Rayquaza
- Average movepool
- Can't check more offensive Kyogre variants well because it gets stomped by Water-type STABs
ORAS Zekrom:
+ OK STAB combination
+ Attack stat still as useful as ever
+ Checks both Water- and Flying-types
- Vulnerable to Ground-type coverage from Mega Salamence
- Suffers from Palkia syndrome in that both of its STAB moves have a common immunity (Primal Groudon / Xerneas) - this makes Choice sets very prediction reliant
- Mediocre Speed tier
- Water-types already checked by the best Pokemon in the metagame
- Fried by Primal Groudon (mixed set can circumvent it somewhat)