Kronos and 
Karg Noloner have Galatic Lore, instead
they now come with the Neutron Scanner.
Mentox now has knowledge of the Structural
Analyser and not Autolabs.
Several others where a little under-powered:
Galis, the 10% financial bonus was hardly
worth the cost in early part of the game.
Now he also comes with the Space Port.
Kimbuzzi gave a 10% increase in farming.
This equated to a mere 1 or 2 extra farming
in the early game. Now he also comes with
Hydroponic Farms.
There are several other additions and deletions
which are not listed here but can be discovered
by playing the game with the new modification.