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I am aware that assassins take far longer and are more expensive to make than Space marines, however their training is superior in every way, but I'm not entirely sure how it is different.

Mainly everything. An assassin's training would be about stealth, infiltration, camouflage, and precision weapons. A Marine's training would almost be the complete opposite.

I would also imagine that Space Marines, like most soldiers, are trained to operate in squads, relying upon one another, coordinating their actions, and watching out that they do not endanger their battle-brothers (friendly fire!).

Assassins on the other hand usually operate alone (except when dispatched as an Assassinorum Execution Force), and will be trained to rely on none other than their own skills and instinct, as well as using their greater freedom (not having to care for teamwork) for more and faster improvisation.

 SoloFalcon1138 wrote:
Mainly everything. An assassin's training would be about stealth, infiltration, camouflage, and precision weapons. A Marine's training would almost be the complete opposite.

THIS. Unless, of course, Alpha Legion...

Alpha Legion is focused about squads though. Recruits are not taken alone, but in squads.

Well, its really going to depend on which assassin temple you're talking about, because they're designed with very different tasks in mind, and none of them are meant to do what Marines do. Well one of them sort of is...we'll get to that. Space Marines, as I'm sure you know, are heavily armed and armored frontline shock troops, who tend to focus on shock and awe raids with small strike teams to overwhelm the enemy quickly.

Callidus assassins focus on infiltration to execute single targets. Most of their training would have to involve deception, stealth, and disguises. This includes learning to use polymorphine to change physical their physical appearance, so they can impersonate literally anyone. They also learn to master various martial arts, and excel at close quarters fighting.

Vindicare assassins are snipers. They're training is all about stealth, evasion and marksmanship. They have to be trained to find the best possible position from which to shoot, to remain there undetected until exactly the right moment, and to not miss with what may be an incredibly difficult shot.

For Culexus assassins, what matters more than training is that they have the Pariah gene. It's a gene which basically makes them the inverse of a psyker. They have zero presence in the warp, and actually drain psykers and warp energy just by being near them. Naturally, they are meant to hunt psykers, and their training would mostly be focused on honing their natural ability to block and absorb psychic power.

Eversor assassins are actually the most like Space Marines, except they single handedly do the same amount of damage as a small marine force, and they do it while on all the drugs. You don't so much train an Eversor as you build one, which I suppose is another similarity to marines. They probably have more implants, physical enhancements, and cybernetic upgrades than they do human bits. All of these are designed to make them insane, rage-fueled, berserker killing machines. They are then injected with enough drugs to kill like a thousand men, and pointed in the direction of the enemy. They have to put them in stasis between mission, because as long as they are conscious, they will murder just everything.