I think there are ways to make cloaking more fun in a WC-type game; you just have to be clever about it. Some ideas:
1). Limited cloaking time (maybe because of a power draw)...you can cloak for, say, 3-10 seconds depending on your power reserves, but then you're visible and have to let your reserves recharge, or your cloaking device "cool down" for a while before you can use it again.
2). Speed/maneuverability restrictions...if you fly faster than 100 kps, or turn too hard, there is a chance that you become either temporarily or permanently visible. Make the probability go up the faster you try to run.
3). You can cloak only n times per mission (perhaps only once), without overloading and cracking your cloaking crystal. Or maybe, to make it interesting, the first time you hit the cload button, there's a 95% chance it works. If you de-cloak and try it again, there is a 60% chance, and a 40% chance you crack your crystal and lose cloaking from there on. If you try it again, the probabilty is more like 30-70%. And so forth. Combine this one with limited cloaking duration, and you have one more "trick" in your toolbox that doesn't become the all encompassing panacea that cloaking in a Dragon was.
4). Cloaking completely drains your guns and shields, so that when you de-cloak you have to evade for a while before you're useful for anything.
5). Have some missiles be cloak defeating, like the modified torpedo in Star Trek VI. Maybe the HS...it would make HS's actually useful for something. And it would kind of make sense...maybe cloaking masks your radar signature and hides the visible light range, but not your IR signature...
6). Let you fire while cloaked, but firing makes you visible for a second (or three), and while in this state your shields are weak, or non-functional, or slow to recharge...
7). Have detector ships that can see you (and allow other fighters to see you) even when you're cloaked. That would make you want to go after them first, so you can cloak with impunity...but then design the mission so there are higher priority targets (incoming bombers, enemy SAR's picking up your pilots, capship missiles) or dangerous ships escorting the detector (powerful anti-fighter missile ships?) that would force you to make strategic decisions.
8). Have a finite number of cloaking crystals availalbe for *the entire game*, so you can choose to take and use one in a particularly tough mission, but then you won't have the option to cloak as often later in the game.
9). Cload and countercloak technology...have some ships carry EMP generators that disable all cloaks in the area for a while, and fire them randomly, or when you don't expect it. Especially consider making them not affect cloaking devices on uncloaked ships, but to temporarily or permanently disable cloaking devices on ships using their cloak at the time of the pulse.
I think you could make some very fun gameplay by mixing two or three of these ideas. And in any case, it wouldn't unbalance the game, or feel as artificial and cheatingish, as the Autoslide in WC3, which always felt to me like a debugging feature the programmers decided to leave available to the user.