Is this for in-game or competitive?
Origin Pulse has more PP and is therefore better for grinding in-game. It also has consistent damage, but in-game that doesn't give it much of a boost over Water Spout because you have the great Full Restore on your side. Competitively Water Spout is a beast in the Rain, but for that you might want to use plain ol' Scarfed Kyogre to make sure you get a max power Water Spout off onto whatever you want to kill. It's good to have a backup Water STAB like Surf in case Water Spout runs out of PP or gets too weak. So, in summary, my advice is:
• Use Water Spout to kill everything on an offensive set
• Use Origin Pulse for a slower, bulkier set
• Use Water Spout to kill everything and bring Origin Pulse as a backup to have two almighty Rain-boosted Water STABs to rain death upon your enemies.