Pro Stealth Unit: The only side that gets Stealth units is the Imperial Remnant, and only in maps that include Honngor, and only post Era 2 onwards. They could be a significant element in ground strategy, letting people scout out units and defenses in advance without having to bring in something like the Heavy Tracker or suicidal Scout Troopers. They could make infantry more lucrative to spend money on as something other then the cheap option to defeat the enemy with. In addition the number of infantry units is lacking, with there only being the semi-unique slash interesting scout, sniper, E-Web trooper, and Jedi subclasses, as far as 2.1 goes.
Con Stealth Unit: A stealth unit would be unfun and unfair to fight against in multiplayer due to spam of invisible soldiers would be annoying if EVERY faction could do it with only having to use one type of building, rather then a specific building and planet. In addition the stealth unit would, if being merely cloned Death Commandos, be overly expensive for a glorified artillery caller. Scouting isn't really important in the game as it's more of a numbers game in the later stages, and scouts would be rather expensive to use in the crucial early game segments.