burn and swallow after reading
Heres my sum total knowledge of intelligence gathering, some of its commmon sense and some its a bit more complex. Enjoy:
Sometimes the most critical aspect of stopping an enemy attack is detecting it in the first place. To that end, techs on both sides have served up a nasty platter of sophisticated systems that are designed specifically for, or can be adapted to the role of, spying. One of these systems, known for it's ability to detect cloaked ships, is the Proximity Sensor. Although it can be used in the previously mentioned role(and should be used in that capacity too), it also tells you when it's near an enemy ship of any kind. Which frees you from constantly checking the sensor overview, just deploy them in a semi-circle about a third of the way between the enemy's Mothership and yours. Every time a enemy ship dares to cross that line you'll hear a calm female voice say, "enemy ship detected." This is your cue to check on precisely what has dared enter your territory. 90% of the time it will only be a scout or a probe, but it will be worth it.
An interesting thing about Cloaked Fighters is that they can stay cloaked, almost indefinitely. You can use that by identifying the enemy's permanent bases and positioning a stealth sentry right in the middle of it. Unless you used stealth attacks in the past or the enemy saw you building stealth craft, he (or she) is unlikely to deploy proximity sensors. This coverage only costs you 80 RU's per base (which is cheaper than using constant suicide 30 RU Scouts), plus you get around the clock coverage, with no waiting until your ship gets in range. This should work great, unless your enemy moves his bases around a lot, in which case your better off the old-fashioned way.
Another wise move is to deploy one or more Sensor Arrays. It will give you precise formation counts for enemy groups that before appeared as only one red dot. It is also advisable to keep five Probes in formation next to the Mothership for immediate precise coverage on any enemy formation. These tips, along with a competent and well informed commander will render even the most oblique enemy schemes transparent.