1. Variety..? Humanity's first contact with the Covenant was in 2525 and the game takes place in 2552 which is 27 years after the first contact with the Covenant. The flood were on the planet G 617 g, which is a Forerunner planet, so you wouldn't really see the Forerunners or the Flood on Reach anyways just the Covenant.
2. That's how Reach ended, all the Spartans on Reach died except for Master Chief. He is known to be the last Spartan alive but there are 17 (in total) Spartans still alive.
There are three Spartan-II's: Linda, Kelly, and Fred which are stuck in the Micro Dyson Sphere at Onyx.
There are also three Spartan-II's, designated "Grey Tea", were said to have been on "fields of battle too distant to be easily recalled."
Of the Spartan-III's (Gamma Company), there are two teams that remain. There is team Katana that is stuck in the Forerunner equivalents to cryo-tubes.
Team Saber is the other remaining team. The team consists of Ash, Holly, Dante, Olivia and Mark. Of them, only Ash, Olivia, and Mark are alive in the Dyson Sphere.
There are also two Spartan-III's (Beta Company) remaining, Tom and Lucy.
So, all together there are 7 remaining Spartan-II's and 10 Spartan III's.
3. It definitely felt like Halo to me.