This isn't about MMOs, it's about real life/pen and paper games. However, some MMO experience might also help understand my point. It's especially relevant for e6, but it does affect how I think about stealth in Rifts.
Two sides are engaged in combat. Suddenly, a rogue comes out of stealth/invisibility and backstabs a dude in the battle (who dies) then retreats, attempting to get out of combat. This happens a lot in big MMO PvP battles. Think about the last time this happened and what you did?
Maybe you were aware of the possibility of a sneaking rogue. The initial arrival of the rogue didn't surprise you, and because you were constantly looking around for him, you spotted him and called him out or attacked him.
But the chances are that he took you by surprise a bit. Maybe you caught him as he got away, sprinting out of range of combat. Even though you saw him, you probably didn't get a chance to engage. He caught you by surprise and your reactions are slow. Now you're aware of him, but he's long gone and you have no idea where he could be. There's also the chance that you simply didn't notice him at all and he got away for free. You might notice later that your pal is dead, but you won't immediately attribute it to the rogue. He probably just got popped by the enemy DPS or something.
Now add in distance to the mix. Even if you're aware of a stealther, a long-ranged attack could come from anywhere and it isn't immediately apparent where those packets of damage are coming from. If he's not hitting you, there's almost zero chance that you'll see him unless you're fully aware of where he could attack from while in stealth. If you're in a situation where there's a lot of cover and he could be anywhere, you're not going to spot him unless he pops out to shoot right in front of you. By the time you even realize someone is shooting, he's probably gone. In fact, the only reason you might know at all is because your dead buddy tells you about a stealthy sniper from beyond the grave (yay voice chat).
If someone is engaged in combat already and a sniper attacks, there's basically 0 chance that anyone not directly getting shot will be able to spot him. In a real battle, you have to be focused on the enemy that's threatening you, especially because you only have one life, can't respawn, and wounds aren't just an issue of healer mana. If you're not engaged in melee with someone, you might have a shot if you're looking at the battle at large, but even then you're probably looking for opportunities to shoot into the combat, flank someone, or zone the enemy out so they can't reach your archers/spellcasters.
Now if there's no battle and you launch a sneak attack with your force, you'll probably have some surprise advantage, maybe get in a round of attacks before the enemy is prepared. However, if you're the only threat and you're sniping, obviously the enemy is gonna be looking for you.
Basically what I'm saying is that characters using stealth weapons like bows or crossbows (or suppressed guns) shouldn't be detected at all if they start attacking after the main battle starts. Other combatants are simply too busy thinking about the threats they can see to reflect on threats they can't. Anyone sniped is going to look for a sniper obviously, assuming they survive.
Magic users can't really emulate this as well since spells have verbal components. How loud verbal components have to be is up to the GM, but I assume they have to be not whispered (they can be whispered in Rifts and make reasonable stealth weapons). Magic item use that doesn't require loud command words or spells augmented with sound-cancelling metamagic effects can probably work just fine for sneak attacks. Even normally audible verbal components might not be obvious if a battle has already begun and the spellcaster is well-hidden. Remember that there's probably a lot of grunting and shouting going on in melee. Battle is pretty chaotic, especially in a life-and-death kinda situation.
Even someone sneaking into melee to kill someone on the outside of the battle might not be noticed immediately. Think about how effective "behind the back" ganks are in SMITE, even though the person is visible on the minimap.
Basically what I'm saying is that without the Quick Reconnoiter feat, characters shouldn't be able to make Spot or Listen checks for free in combat. In Rifts, you basically need Intuitive Combat or Eyes of Zandragal active to have a chance of detecting any sort of stealth attacker, and even then the attacker needs to be in your limited range. Zanshin also works (as does CK tech-sense) if the enemy is targeting you. In Rifts, I might consider allowing sixth sense to detect incoming backstabs or snipers (it probably does).
What does this mean for e6? Well, say a party of fighter, cleric, NPC allies and invisible bard (singing) enter battle. Obviously the bard is there, he's singing. Ranger is off in the bushes looking for the target of opportunity to enter the battlefield, and he locks and loads his bow and takes his shots. Nobody should get a check to see the ranger except the target (assuming he's alive after getting shot) and any target's bodyguards specifically ordered to defend the target AND not currently engaged in melee. Some people might be looking for the invisible bard, they are actively making listen checks (instead of attacking visible characters) to try and find him. They probably won't hear the ranger though; they're trying to find the invisible bard they know about.
That's about how stealth should go; known stealthy foes can be checked for (takes actions? move or standard? I think move?), unknown stealthy foes shouldn't be checked at all. The Quick Reconnoiter feat fixes both of these issues; it specifically allows a character to make perception checks passively during combat, because the character is constantly making little assessments about the battlefield while he or she is fighting. Some special class abilities, particularly bodyguards or counter-terrorism units might have something similar.