AFAIC, the whole spying "concept" relates much more on the actual amount (or even pace) of information a player gets about races; sure, the agents DO add a certain dimension with place/nullify - but that's
spending BCs as a one-way ticket to economy variables. I often wished for a sort of
thief instead to steal some money!
What lacks to this feature is a "true" infiltration set of options;
demolish buildings,
sabotage ships & productions,
subdue citizens by propaganda stuff,
examine & report statistical hints of any enemy properties/values directly from nearby planets (Zeroes, anyone?) in a type of outpost spy-base,
etc. And the above theft activity.
Then, you'd have
A more active spy - both worthy of its cost (evergrowing) and highly adaptable skills (again, with some techno/upgrades). Think of a rather unique super-hero (somehow) which gains experience through missions, provides support to invasion troops, stands as an alternate governor-type for Knowledge & Research, even could twart most Mega-Events (sometimes, i'd want to revert (partially, totally, at my discretion) the Jagged Knife right back where they came from, kick a few Pirates' butts and slice a couple of PeaceKeepers' throats!) and - so on.

- Zyxpsilon.