Xilk made a nice post about this over on the FFXIAH forums.
After reading his suggestions, I'm really partial to having 2/5 Beast Affinity - it gives us access to Presto Julio, Swift Sieghard, Mailbuster Cetas, and Audacious Anna at 99 cap. It'll vary based on server, but having access to an inexpensive Vermin, an additional Plantoid besides Flowerpot Merle (I find Discreet Louise to be a rare find on the AH here), and two alternate Lizard-types is beneficial for Killer Instinct users. Presto Julio can be somewhat rare on the AH also, but Soporific is a nice tool if you're able to snag one.
Group 1 Merits can be tailored based on your play style. It'll partly depend on the sorts of events that you do with your BST. At level 90+ when you can wear Monster Trousers +2, I find the Reward timer usually isn't an issue. If I'm entering a situation where I know I'll be riding the Reward timer, I'll bring Dawn Mulsums to bridge the gap (or if it is safe/inexpensive to do so, call a new pet). I think merit selection here is largely a decision between Call Beast timer and Sic/Ready timer, since Killer Effect merits are quite attractive with Ferine Gausape +2. Personally, I'm more of a glutton for Sic/Ready so I have greater flexibility with regards to 2/3-charge moves like Fantod, Wild Carrot, Blaster, Charged Whisker, Roar, Purulent Ooze, Corrosive Ooze, Tortoise Stomp, Harden Shell, and Noisome Powder. When I throw some of these moves into the mix, there are times when the Charge timer can't keep up with a pet's TP gain - if this is a non-issue for you, then Call Beast is a fine choice as well.
The times when I wish I had CB merits are few and far between, but on those rare occasions I have a pang of regret in my heart. Situations where your pet gets doomed, or otherwise 1-shotted or killed by a powerful foe before you have a chance to react... This happened to me yesterday in a low-man Yilbegan attempt, haha. Though, if you're mostly doing Dynamis/Sky/Sea/other older content, you'll generally be okay with regards to pet survival, I think.
Anyway, my personal recommendation boils down to... Group 1:
[Call Beast Recast]/[Reward Recast]/Sic/Ready
[Killer Effects] 5/5
Lulz. Group 2:
[Feral Howl] 1/5 (Dynamis proc/Claim tool/Occasional Stun)
[Killer Instinct] 5/5
[Beast Affinity] 2/5 (Access to all post-76 pets except CraftyClyvonne and NurseryNazuna)
[Beast Healer] 2/5 (Adds +4 Regen to Reward when enhanced Monster Gaiters +2 are macro'd in)
It's easy enough to swap'em around later if you find that a particular combination doesn't work for your play style. :) Best of luck.~ Edited, Apr 25th 2012 8:50am by Bookmarku