You'll get Emblems, instead of Marks of Valor, for the VA-level version... The in-mission drops are all drawn from a higher-level loot table (meaning: you'll get more Mk XI gear, rather than Mk X... NOTE: The Purple (Very Rare) reward drops that you get will ALWAYS be Mk X IF they are gear with the [Borg] trait... Other gear 'should' be drawn from the normal, higher-level table.)... As NeilCell pointed out, you'll get more Merits, BOff points, etc.
Aside from that, the end-of-mission reward (the Assimilated Subtranswarp Engines) is always the same, regardless of which version of the mission that you play.