Have won this several times with different configurations, but all based around the general premise of ranged damage. For a non-zerg setup, this is the logical way to go due to the properties of the mob.
General setup: tank, DDs (both for Seed Crystal and the spawned Seed Thralls), stunner (Stun spell, not Head Butt or Violent Flourish), and additional support/healing.
Suggest: PLD/RDM for tank. Others should work, but Seed of Nihility will preclude using many JAs. Being able to spam low MP, higher hate spells is preferable. High magic defense is nice too.
RNG, SMN, COR, or viable /RNG jobs for DD (SAM/RNG, THF/RNG, NIN/RNG, etc). Evasion is very low, making it easier to utilize /RNG type combos. Elemental magic damage is severely reduced, making BLM or SCH ineffective in this role, Quickdraw damage seems fine though. SMN is perhaps the most preferred here, given their basically hate-free damage. RNG and SAM/RNG I have gone with eventually get drawn in and have to throttle damage back a little, plus they need to run in to WS.
Seed Thrall handling can be done by nearly any job. Preferable if they have a way to pull the Thralls off of your tank, and a way to either mitigate damage or restore the small amount they'll take. It'd be nice if they can also contribute to other aspects of the fight too, but not crucial. BLM is capable of filling this role, along with stunning or backup stunning. Without multiple forms of refresh, however, they may become taxed for MP.
For support/healing, it depends on what you have. RDM/DRK excels here as a stunner, healer, Refresher, etc. WHM/DRK or similar should also suffice. Self-Haste for recast, use good gear, and Stun should be up every time. BRD is decent for Ballad and potentially for ranged attack. COR is preferable, as they can DD both the Seed Crystal and Thralls, enhance pets if present, and so on as well.
The general strategy here is to avoid being in AoE radius as much as possible. Stun -ga IIIs, nothing else should hit anyone but the tank (ideally).
Particular jobs can vary, but this premise does work, and quite well.
The Seed Crystal is planted in the center of the BC area and does not move. It does AoE TP moves centered around itself, and casts -ga III spells, which are centered around whoever is targeted.
It doesn't do melee damage.
It will use Draw In repeatedly on whoever has hate.
There are several spots in the BC area where the party can stand and be out of AoE radius from the Seed Crystal. The top platform where you spawn in, along with the far corners from the entry location at the very least. As a suggestion, just stay on the platform where you spawn in.
Have your tank move in and blow whatever JAs they may have for hate. Their timers will be reset as soon as Seed of Nihility is randomed up, so best to make use of them ASAP. Most likely, they'll be drawn in on their first action.
In order to avoid Seed of Deference (Charm), the tank should run away from the Seed Crystal. It has a very short range, so this -should- prevent them from being charmed, outside of extreme bad luck. Due to the generally very frequent Draw In, the tank will spend most of the fight running away from the Seed Crystal. As a suggestion, have them run back towards the rest of the party. This keeps them in range for heals/Refresh/etc the entire time, and makes it much easier to pull Thralls off of them.
The only real reason for a tank -not- to run straight back to the party would be due to -ga IIIs. The Seed Crystal does not seem to possess any Fast Cast (or if it does, nothing significant), so there's plenty of time to Stun its spells. It also has an interval between casts, which should be more than adequate for the recast timer to be up again.
Obviously, do what you can do reduce recast. Keep in mind as well, if your tank is casting, and they get drawn in, their casting animation may make it look like the Seed Crystal is casting. Better to watch the log (or check it) than the animation.
Either way, stunning -ga IIIs is easy, and few, if any, should get past a competent stunner. The effectiveness of keeping tank/Thralls easily reachable by the rest of the party outweighs the slim chance of getting hit by the nukes.
Seed Thralls are your other main factor. Having one person who will consistently grab these and kill them is good. They don't hit hard, and have little HP. Still, you want to kill them quickly as the Seed Crystal may pop more, just depends on what is randomed up. If you get multiple out, have your ranged DD shift to helping with them.
Otherwise, just do ranged DD to the Seed Crystal. SMN I have gone with just used Predator Claws. As mentioned, ranged attackers may need to throttle damage as to not pull hate. Since WS range is closer, try to wait on a TP move to be used, run in, WS, and then run out.
At 50% (and below), Seed of Judgement is available to be randomed up. This can do a significant amount of damage, along with Knockback. All the more reason to avoid being within AoE range unless absolutely necessary.
With two solid ranged DDs + necessary support, and keeping people appropriately out of range to minimize damage taken, should take it down in 15-20 minutes with relative ease.