The number of targets hit by the Matter Conversion Beam has been decreased during Phase 2 and Phase 3, on both Normal and Elite versions.
On Elite, the following additional changes have been made:
Reduced the max number of Fragments that may be present on the map from 12 to 9.
Reduced the spawn frequency of Fragments slightly
Reduced the Entity's regeneration rates
These are all unnecessary changes.
The single biggest change which could be done for both Normal and Elite is sorting out the Damage Reduction Aura/Bug for Crystalline Shards and Tholians. This Bug/Feature doesn't make the mission challenging, just tedious.
It feels more like a bug because the Shards/Tholians exhibit the same damage reduction behaviour as the Crystalline does during it's Absorption Phases, except this effect is almost always present unless the Shards/Tholians are 8-9+ km away from the Entity.