Dat capsule mechanic: The moment the capsule's hull is damaged in any way -brain spike, hyperlink upload, and depending on a number of facts, you awaken in a new clone. I imagine these mechanics apply to boarding too. Which means if you're a capsuleer looking to capture another capsuleer, you have to disable the capsule from being able monitor it's integrity, or disable the internal grid/sensors which monitor it's exterior walls. And this is after disabling the means to eject (which occurs automatically in the event the ship is fixing to go up).
1. Stun the capsuleer, or simply disable ejection.
2. Disable capsule's onboard integrity sensors.
3. Pull capsuleer free from the wiring which connects them to capsule, starting with the cranial wiring (pull the wrong wire and the capsule may still spike the brain and kill/send the capsuleer elsewhere).
Do these three things and you'll have yourself a free capsuleer.
Mind you, this is a lot of godmodding in an RP and very bold, for any character willing to play victim is looking at total vulnerability of their character. You kill them outside their capsule, there is no respawn, there is no wake-up. There's nothing left for them to do other than consider your RP not canon to their lore as means to save their character.
Of course, if a capsuleer is worrisome of these potential risks (like I tend to try to RP Isis), you make an extra note to voice the secondary measures you have in place to prevent such things. For example: A protocol which in any moment you attempt to eject and are unable to do so, your capsule brain spikes on the spot.
Yeah, I had never actually thought of having that aspect of a story. In my boarding situations, the capsule is left alone and whatever the aggressor wants is taken off of the ship and leaves the actual egger alone. Capsuleer keeps ship itself and themselves untouched, loses cargo/crew, etc.
For most mortals, I assume that would be the case. Lack of understanding the very advanced technology of the capsule or even a capsuleer's ship is a common thing that would push most pirates away from daring to try and board a capsuleer's ship. Especially if there's a prospect of the ship being used against the aggressors (such as gravity being reversed, venting decks, etc. etc).
That's where a capsuleer might develop quite the ego. Boarding a capsuleer's ship with intention to pirate a capsuleer would be nearly unheard of in New Eden (that's like thinking of a single NPC or group of NPCs being able to lock down a capsuleer's ship in say… a mission). Talk about risky business, especially since every capsuleer's ship is built from a separate or independent party (where we build and seed ships to the market).
There's no perfect map of a capsuleer's ship considering that fact, nor do we know where the SCC pulled their crew from (or if they swapped crew for say, an elite Caldari Navy crew during the quest of RPing their characters), how potent is the fighting force, and the capsuleer's defenses (both digital and physical).
NPCs are far better off trying to board another NPC's ship, as the interiors would be more constant and significantly easier to overcome (not to mention tailored for people to go more freely around the ship compared to say, a capsuleer's ship).
However, it wouldn't be uncommon for less knowledged NPCs trying to board a capsuleer's ship, thinking it's not a capsuleer's ship, realizing late they bit off more than they could chew… Dat potential ego that might develop in the victim capsuleer after a few occasions repelling or trapping aggressors during these occurrences.
Even considering other capsuleers. Most capsuleer aggressors are only after loot and killmails, careless of the technology that makes them who or what they are… let alone how to use that technology against them. There's very little reason to fear capsuleers for doing anything more than the typical. An even additional backing fact: a capsuleer also almost never likes relying on a crew, and many simply deny their crew even exist (as witnessed on the EVE Online forums).
So prospecting a capsuleer wanting to use boarding teams to seize hold of another capsuleer alive… talk about something beyond unheard of.
But of course, you hang out with characters like ours these days, you tend to be exposed every day to statistical out-of-the-box-thinking freaks. xD