Just as a short explanation for non-EVE people: T1 or "Tech 1", are all "normal" ships you can build/buy in EVE, like common frigates, cruisers, battleships and so on. T2 ships are more advanced ships, normally specialized to do something better then a T1 ship. A T2-logistics ship is generally better at saving other ships than a T1-ship, for example.
T3-Destroyers or Tactical Destroyers instead have different "modes" they can change after a short cooldown. Modes like Sniper-mode for long-range shooting or Speed-mode to get out of dodge fast.
T3-Cruisers, the older T3-variant, went down a completely different path. First off, you need not only the hull, but also a set of five subsystems (defense, electronics, offensive, engineering, propulsion), all build and sold separately by players to get a full ship. The four different cruisers (each for one of the four main races) all have different subsystems to choose from. Sometimes with some overlap, sometimes a certain subsystem will work differently or will be unavailable for certain races. The Gallente Proteus for example can use a propulsion-subsystem to warp faster, but the Amarr Legion doesn't get a subsystem with this ability.
This mixing and matching of different subsystems generates completely different looking and working ships depending on what you chose.
Which is the idea: If you want a cloaky, stealthy ship, just take the necessary subsystems and your T3-cruiser is now stealthy. If you want a death ship killing everything, you have subsystems for this, too. The funny thing is, right now CCP is working on a large-scale rebalance of all T3-cruisers, thanks to some wonky balance. Some combinations of subsystems turned out to be insanely strong, while others are underused or not very usable at all.
If you make cloaky T3s, for example, you'll notice you have to fight really hard to make a Legion (the Amarr-T3) cloaky and stealthy and fighty as all the other ones. The reason here is mainly the covert-ops subsystem which allows the use of a covert-ops cloak (which allows you to warp around cloaked and practically invisible). All other 3 T3-cruisers have a small damage-bonus to offset the serious gimping a truly stealthy T3 has to endure. This means most T3s can have all the stealth and scan-things and still have at least a comparable strength to a destroyer or T1-cruiser. The Legion covert-ops subsystem however, hasn't. Instead it has a bonus to capacity use, which means the laser-weapons a Legion uses will draw less energy from the capacitor, making the ships more able to not suddenly run out of energy at the worst possible moment.
This also means indavertently, that the DPS of a stealthy Legion is shit. If you're careful with crafting your perfect stealth Legion, you can get some sort of "good enough"-fit with less EHP, better active tank and about equal DPS compared to the other 3 T3s. This fit by the way isn't interdiction nullified, which means tough luck if you end up in a bubble.
The other T3s are vastly superior in that category, because they can get, with the same concentration on stealth, more EHP, equal or more DPS and of course they can laugh about bubbles and just warp away. Only the active tank remains superior, thanks to the synergy of combining several subsystems helping with supplying the energy-hungry armor repairers with the nanobot injector, a subsystem with huge bonus to active armor repair.
This sadly won't help you if you can't get through your enemies' tank fast enough, of course. Two stealthy Legions against each other would be the most saddest thing because of this: Both would never run out of energy and would also both never break through each other's tanks. Also someone would drop a bubble on them sooner or later. Then both die, the end.
On the other hand, some Legion-set ups are ridiculously good. But that's the thing: Some subsystem combinations are incredibly good, some rather bad. CCP wants to change this and as someone who generally has no use for the insanely overpowered set-ups anyway, I can't wait to see what will happen.
Another problem T3s have: Since their entire look changes depending on subsystems used, not all looks are visually attractive. To be honest, most T3s are unbelievable ugly. And when not ugly, the T3s are one of the strangest and most unique looking ships in EVE.
|Cloaky Legion: Weak as a kitten, but can take a punch. And sloooooowwwww|
|Stealth Loki: More EHP, less tank, but looks sweet. Also more DPS, because of course it has.|
|The Cloaky Potato (Sorry, Proteus): With blasters easily the highest DPS of all|
|Stealthy Tengu: Everyone wants the Tengu. The Tengu is God. I hate this weird ship.|