Cloaking plays in important role in Star Trek. It is a core feature for both the Romulans and the Klingons, and finding a cloaked vessel often was the key element of an episode. Sadly, due to limitations of the Armada 2 engine also in Fleet Operations, detection was rather simple - a sensor station detects all cloaked vessels in their radius - a system that made cloaking mostly useless.
But that has changed! New cloak detectors will work similar to what you have seen in the shows. They will emit a Tachyon Ping in a given interval, which might detect cloaked vessels nearby - however there is a chance of failure. Those pings - while physically invisible - are displayed with a small "sonar-like" graphic animation, which allows a player to check his detection net with ease, in order to identify holes or weak spots.
Life would be so easy, if there weren’t those nasty Romulans. Yea, I’m sure you already guessed it. They advanced their cloaking in the past decades quite a bit! Some particular Romulan vessels have been spotted, that utilize a special, top secret cloak.. which is undetectable by normal Tachyon pings! Those vessels may slip through your whole cloaking net! As if that wasn't enough of the nasty tricks, there are also some new or modified special weapons that interact with cloak detection, like the new Stealth Field, which will disable Cloak Detection in a certain radius.
But no need to panic! There also is a way to detect the undetectable. Namely: Graviton-Tachyon pings. And that’s something no cloaked vessel can avoid.. well unless using some kind of phase cloaking, but that’s another story. Sadly detectors which are capable of emitting those 'super pings' are quite expensive and usually found late in an empires technology tree.
As you see, we took a lot of time to underline cloaking and make it more fun and usable - and more important for our two 'cloaking empires'. Gameplay wise this two-stage cloaking and cloak detection allows cloak to be used effectively even in late games and gives cloak detectors a major role. On the other hand, it has to be balanced in, of course. You will see a lot of changes for both the Romulans and the Klingons. While the Klingons got more offensive oriented and don't feature much advanced cloaking, the Romulans got focused on nasty traps and cloaking combat, with quite a few vessels that will make your foe want to deploy graviton-tachyon-pings.