OK, I'm gonna jump in uninvited with an F of a lot of points here, some of them may be misguided or uninformed (this coming from the background of Downfall as well, so I'm not sure how canon):

1. Kendra is a government agent, but what exactly is her mission? How much was Kendra manipulating Isaac Couldn't a message have been sent to the Valor without being aboard the Ishimura? Did the gov. want to destroy the marker or retrieve it?
2. What was the purpose of the second marker? What did the government hope to gain from it? Were the Necros there before it? Was it designed to keep them there?
3. What happened to the original marker? What did it do? Where is it now? Who built it?
4. Did the hallucinations come from Hive Mind or Marker? Do Hive Mind and Marker have the same agenda?
5. Were the Unitoligists (loved the parallels with Scientology) really just a misguided group, who'd somehow got wind of the original marker and formed a religion around it, or is there something more sinister at work in its upper echelons?
6. Was Hammond really innocent? Did he have his own agenda, other than repairing the Ishimura and getting the Hell out?
7. Does Necrole kill Isaac at the end or could he have fought her/it off?

I realise that many of these questions are unaswerable as none of the elements of the Dead Space franchise provide the information, but it was all on my mind and I was wondering what people thought

My views are that the government found Aegis 7 and the Necromorphs and built the marker to leave them dormant on the planet protecting the rest of the galaxy; if this is the case then it is possible that the original marker, which was found on Earth was designed by an ancient alien race who had found Earth and observed humanity's violent and cruel tendencies and left the marker there to stop humanity spreading throughout the galaxy, but it only succeeded in slowing the human race not stopping it entirely, meaning that eventually the Necros could break free of the marker's power (of course this all just conjecture).
Nicole was dead before Isaac arrived at the Ishimura. The Nicole seen throughout the game is a hallucination; the locked door which she opens is also a hallucination, as is the attack by Necros. The game over is triggered because Isaac believes entirely in the hallucination and believes there is no way forward, coupled with the apparent death of his girlfriend he would be distraught and despondent and easily ready to admit defeat (i.e. give up).
The marker was designed to keep the Necros on Aegis 7 therefore manipulates Isaac into returning it to the planet's surface to fulfil its purpose. The Hive Mind tries to prevent this to protect her newfound freedom.

I really hope Isaac is alive so he can come back for Aliens style sequel where no one believes him and he has to assist the military, mainly because I think it would be cool to see some squad based survival/horror and maybe some co-op, but that might take the fright out of it.

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I hope they explore the moseleum ship fleet that Isac's Dad helped construct. That could be a really good setting and story for the next game. Then you could have necromorphs that are already processed into more advanced enemy units rather than the mindless abominations of the first game.

Isaac is not Dead, this has been confirmed during one of the Dead Space: Extraction press releases, hinting heavily (and all but confirming) Dead Space 2. They said Isaac is definately not dead.

The reason it ended like that, like a lot of products that don't know if they will be getting a sequel, is to convinently allow for both depending on what happens in the real world when it's released. The product sells badly and no sequel is made, then it was real and he's dead. The product sells well and gets a sequel, it was a hallucination. :

"@The_A_Drain said:

" Isaac is not Dead, this has been confirmed during one of the Dead Space: Extraction press releases, hinting heavily (and all but confirming) Dead Space 2."

Oh, Dead Space 2 was announced a long, long time ago(Last year, I believe. I even think they've confirmed that it's gonna be a trilogy). We just didn't know if Isaac would be in it. "

1) To retrieve the marker. When she was sent, the government had probably hoped the team would arrive at Ishimura before all hell broke lose. If they known an outbreak had already occurred, i speculate they would have sent Valor in for an immediate attack and not even go through the facade of sending a repair team with an embedded agent on-board.
2) I think the second marker was manufactured to trap the necromorphs on the planet. I am confused though on how a man-made replica of the marker can still have the same psychic effect on humans as the original marker. The government must have backward engineered how the original marker worked completely to build a marker copy that worked as well. Plus the marker appears sentient which makes it even more weird that its a man-made copy. 
3) I think the original marker is still in the hands of the goverment being studied. 
4) The Marker was behind Isaac's hallucinations. 
5)  A group that believes the necromorphs are the next stage of human evolution are extrememly dangerous  despite their pure intentions. I didn't see any records or audio tapes that mentioned if the church leadership are true-believers or cynically pulling strings for a different purpose. 
6) Dude was just doing his job. Although if I were him, I wouldn't have left Isaac's side. Engage necromorphs Army of Two style. 
7) Like everyone else, I heard that Isaac isn't dead. I agree with the_A_drain on why the ending is in there. It was probably just an hallucination brought on by stress and guilt since I thought the necromorphs were all inactive now that the marker had been returned to the planet - and the hive mind getting slammed by the planet core. 
 
I'm not sure how you implement a co-op or squad mode and keep the same atmosphere to the game. I think the dead space universe is rich enough to allow for an awesome franchise though. Since the Ishimura was as much a character as Isaac and Kendra, the sequel would need a compelling environment as well. I like super_machine's idea of a mausoleum ship.