I like the concept !
2 things are there which tickle me.
First: The alien which sieged earth arrived 15 years after the homing bacon fired. How did they get there so fast, Iīm not quite sure but wouldnīt we be able to see their planet if they where only so far away (sorry if im making an idiot out of myself right now ^^)
Second thing, which is just a small concept adjustment:
You can make the obelisk telporters. The cloning system is kind of redundant, as it exists on the ship, and on the planet surface (as far as is get it). If you make the obelisk a power source and a telporter (obelisk<->obelisk) you can put all the cloning into the ship and give them another obelisk onboard (for research i.e.) they can use this one to dispatch the clones to any other obelisk on the planet surface.
regards!