1: Anima is not acquired through customising weaponry or anthing, he's acquired by accessing all the hidden locations in all the main temples in the game. If you fail to do this the first time round, then in two cases - Besaid and Macalania - you will have to fight dark aeons in order to access the temples. once you have used the destruction spheres to find the hidden areas in Besaid, Kilika, Djose, Macalania, Bevelle and Zanarkand (you'll have to return to Zanarkand a second time to do that) simply find the temple of Baaj (the sunken ruins from the start of the game) using the navigation screen of the airship and looking in the south-western sea until a new destination appears on the list. go there, activate all the glyphs, and Yuna will be able to pray to the faythe for Anima.
If you fail to access all of those hidden chambers the first time around, then the chambers at Kilika, Djose and Zanarkand can all be safely visited, but Macalania and Besaid are guarded by dark aeons, and you can never revisit the temple at Bevelle after acquiring Bahamut, so make sure you clean the place out the first time through.
I think what you're referring to in your post, however, is getting hold of Auron's ultimate weapon. To do this, you need to get up Mushroom rock road, yeah? it is possible to get past the group who summon those dark aeons by hugging the extreme left of the path as you move past them. Stay far enough left, and you won't get close enough to trigger that fight sequence.
2: I've defeated all the dark aeons bar Dark Anima and Dark Yojimbo, although I confess that this is not due to any particular skill on my part - I just summoned Yojimbo and prayed for a "Zanmato" attack every time. This tactic will probably work on Penance as well (the boss you get to fight after defeating the dark aeons) but I haven't got so far as to try it yet. It's more luck than skill, frankly.
The key to getting Zanmato on a regular basis is this - mercenary points. the more kills Yojimbo scores against powerful opponents, and the more you pay him, the more points he'll accumulate. Being stingy with the gil, sending him up against inferior fiends, letting him be defeated, and not using him very often will lead to a small number of mercenary points, leading to weak attacks such as Daigoro. Paying him loads, presiding over victories against honourable, strong opponents, making use of his services and summoning him with a full overdrive guage will lend to his mercenary points. The more points he has, the more powerful the attack he will use. Send him up against potent fiends to build up the number of mercenary points, Grand Summon him, pay him at least ten thousand gil, and the odds are better than 90% you'll get a Zanmato. If you don't, go away, beat up a few powerful fiends, come back and try again.
Towards the end of the game, when you're actually looking to fight dark aeons, you really should be so powerful that the only places in which to coach Yojimbo's skills are Sin, and the Omega Dungeon. Otherwise, the fiends are too weak and his supply of mercenary points will slow to a trickle.
unfortunately, the game gives you no feedback on how many points he has, nor how likely he is to perform a given attack, so it's more intuition and practice than an exact science.
I did, however, succeed in beating Dark Ifrit without resorting to that tactic - I pounded him with every Aeon overdrive going (with the obvious exceptions of Ifrit's and Yojimbo's), and then brought Auron, Tidus and Yuna forward, using their ultimate weapons, and shields with Auto-phoenix, auto-haste and SOS overdrive. Yuna's role was, basically, to maintain as many "auto-life" spells on everyone as she could. It was a close-run thing, but I eventually did take him down by smacking him with every overdrive I could manage whenever it became available ("Blitz Ace", in particular, is invaluabl - with a maxed out strength stat, Tidus will cause about 100,000 damage every time it's used, assuming you pull it off well. Auron's "Tornado" is also useful.)
3: I enjoy FFX-2, although it is a much different game -cuter, less serious, and much less plot-driven. One of its strengths is that the combat system is, I think, somewhat better. We see the return of ATG bars, for one thing, and the "dressphere" system - in which you assign multiple classes to the characters, which they can switch between as the situation dictates - is much better than the Sphere Grid of FFX.
Speaking of which - some hints:
One of the side-effects of the sphere grid is that characters can go wandering outside of their own disciplines, or use special spheres to learn a few extra skills. One of the most powerful (I found) applications of this is that, if you train pretty hard, you should be able to divert Yuna off the white mage path for a little while somewhere around about the Mi'ihen highroad, and have her learn the level 2 black magic spells - Fira, Thundara etc.
This is an incredibly good idea - as a white mage/summoner, Yuna's "Magic" stat is significantly higher than Lulu's at that stage in the game, even if the two are of a similar standard. meaning that, when outfitted with black magic, Yuna does much more damage with the same spells than Lulu does. This means that you get a combination black/white mage/summoner - a deadly combination truly befitting a summoner, as Yuna becomes able to scour fiends from her path, heal her guardians AND bring the aeons in to fight. You effectively eliminate the need for Lulu on the lineup at all, and can safely leave Yuna up there in front, secure in the knowledge that she can actually pull her own weight.
second - Wakka and Kimahri are basically useless. Kimahri is actually dismally weak, having no kind of a defined role at all, and with sufficient training, Tidus quite happily fills the bug/bird-killing role that Wakka theoretically assumes. Of the two, Wakka is the more useful, but once Auron arrives there really is no reason to keep either of these two on the front line.
Rikku - Don't underestimate the little one. Some of those machina can really hurt, especially if you're running low on hit points, but she can take any of them down in one hit. also, if you manage to find a good way of charging her overdrive guage up faster, "combine" is really neat. I reccomend combining grenades (which are essentially useless after Macalania anyway) with spheres to produce blasting mines, which do a bit more damage, but also blind and silence anything that's not immune to those two effects. Also consider using a few spare special spheres to give her access to some black, white and supportive magic (I favour drain, cura, flare, the four "nul"s, reflect, hastega, doublecast, osmose and maybe holy)
most importantly, however - completely ignore her ultimate weapon, and instead have her imbue a somewhat more basic weapon with properties such as "sensor", "First Strike", "Auto-haste" and (my personal favourites) "Stonetouch", "Stonestrike", "Deathtouch" or "Deathstrike".
Tidus and Auron - The two most powerful characters in the game. A little piece of advice for Tidus - if you're playing on the advanced sphere grid, Tidus' starting position is very close to Rikku's. I advise taking some time out to ahve him nip over and grab "Steal" and "use" - you should be able to achieve this before the end of the Kilika chapter. Also importantly- regardless of which grid you're using, Tidus's last reccomended skill on the grid is within easy striking distance of Auron's suggested path... along with all those juicy "Strenght +4" nodes. move him in there after completing his own path, and Tidus will quickly come to rival and, indeed, match Auron in destructive potential (more so, in fact - he's faster and more accurate, and his best overdrive move does waaaay more damage). Don't be stingy with Tidus' overdrive moves - he learns new overdrive moves by executing overdrives (success optional) so have him wig out on his enemies as often as possible, so as to learn "energy rain" and "blitz ace" as soon as possible.
Where auron goes after completing his reccomended path is up to you, really, but I'd advise sending him to go explore Tidus' realm - he really needs the extra speed and accuracy that's available in there. Avoid magic like the plague, though - he needs those MP.
Towards the end of the game, my chosen lineup consists exclusively of Yuna, Tidus and Auron - who are, after all, the main characters - and the rest are largely just hangers-on (less so in Rikku's case). Have them train long and hard enough in the Omega dungeon and they'll quickly begin to really rock. ultimate weapons and auto-phoenix armour all the way, and they become well-nigh unstoppable.
good hunting!