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Rudra and Abyss are the two best ones. At level 99 they're about equal: Rudra has slightly better auto attack damage on average (69 points IIRC) but Abyss has +10% crit rate. That partially catches up the damage difference but more importantly, it means faster party gauge building, more burst affinity chances and better tension. Personally I slightly prefer Abyss but the difference is pretty slight overall. At lower levels, Abyss can actually even be better average damage wise since its max auto attack is better. IIRC at level 84 or below it averages the same or better damage as Rudra, at which point it's far and away the best.
The other three are arguably all worse than the standard Replica:
Agni's slightly better defences and block just aren't very useful for Shulk, a damage focused character, and the drop in crit rate and damage are bad. Dogma has only two gem slots. If you really want a higher crit rate that badly, use Abyss and a Critical up gem. Saga has some niche builds it enables for tank Shulk, but in most cases it's bad - low damage compared to the others, low crit AND only two gem slots.