Ok, here we go *has beaten everything but Penance* Like you said, to get Anima, you need the Destruction Spheres from all the temples.
As far as I remember, there are only 2 temples that are guarded by Dark Aeons, Besaid (Dark Valefor) and Macalania (Dark Shiva).
To beat these 2, Shiva especially, you need to max. out some stats, namely evade and accuracy (if I remember rightly it's the Fenrir and Hornet species creations at the arena that drop these spheres). You might wanna raise your strength to at LEAST 200 as well so you can consistantly do max. damage (Juggernaught species creation I think that has those)
Break HP Limit is essential for these guys, and will make Dark Valefor a LOT easier, since his normal attacks only do 9999, so with Break HP, you'll survive them. Break Damage Limit is also essential, unless you wanna spend forever fighting these guys.
So now, the strategy...
Raise Wakka's strength so he constantly does max. damage, and make sure you have his Celestial Weapon properly powered up (Weapon from a bar in Luca, Saturn and Crest from the Auroch's locker room and as a Blitzball prize). You also need his Attack Reels overdrive (also a Blitz prize).
Get Wakka to his overdrive, and make sure you get 3 "2 hits" reels. This will result in 12 shots for Wakka ((3*2=6)*2 for matching all 3 = 12 shots) at 99,999 damage each, and should give you a very DEAD Dark Valefor.
Dark Shiva however is a little tougher. Use Wakka's Attack Reels again, as well as Tidus' Blitz Ace. If she gets to an Overdrive, use an Aeon to take the hit. Auto-phoenix armour is pretty much essential here. (Customise with 30 Mega-Phoenix, bribe from Spirit in the Cavern of Stolen Fayth for about 200,000).
Basically, if you follow this setup, those 2 Aeons at least, shouldn't be a problem.