Well, it's never been stated on the show, but it seems to me that cloaking tech wouldn't really work
with most kinds of Federation ship. We know that cloaks aren't perfect, that on the one hand they take a lot of power to maintain, and on the other hand, a ship has to minimize its power usage to keep emissions to a minimum (like a submarine on silent running -- since, of course, "Balance of Terror" was an homage to WWII submarine movies to begin with). So that creates a problem of diminishing returns. The ships that can best make use of cloaks are stripped-down, austere battleships that don't expend a lot of power on nonessentials -- like Romulan and Klingon ships, or like the Defiant
. But most Starfleet vessels are multipurpose craft serving as science vessels, diplomatic couriers, and the like rather than exclusively as combat or defense vessels. They expend a lot of energy on research labs, crew comforts, recreational facilities, and so on, and that would make them harder to cloak.
So cloaks aren't really a pure advantage to the side that has them. There are certain inescapable limitations they impose on their users. Or at least, there should be, though the 24th-century shows kind of ignored this common-sense conclusion by putting cloaks on enormous ships like Romulan D'Deridex
-class Warbirds and those gigantic Klingon dreadnoughts. Still, it stands to reason there are some tradeoffs necessary, restrictions on power usage in order to allow such comically oversized ships to cloak their emissions effectively. Cloaked ships are specialized to do one thing -- sneak around for the purposes of espionage and surprise attacks -- and beyond that there's not that much use to them. Starfleet's design philosophy is built around adaptable, generalist vessels, and they probably feel that versatility is a greater advantage than the rather limited benefit of invisibility.