I have received the Escape from Goblin town starter set and I have ordered the The Hobbit Rules Manual from GW and I don't know if I should collect either Mordor or Moria? Which force do you like to use more Mordor or Moria? Which force is easier to paint? What are the pros and cons of both forces? Can I use the trolls (Tom, Bill, Bert) in a Moria army as well as the goblin king from goblin town or do I have to buy another goblin King?

You can ally all Evil factions, so you can have an army with both Mordor, Moria and Goblin Town models, but you will need Heroes from each faction in order to include Warriors from that faction.
For example, you can have the Goblin King with a warband of Goblin Town Goblins allied with a Moria Goblin Captain with a warband of Moria Goblins allied with a Mordor Orc Captain with a warband of Mordor Orcs, but you couldn't have a warband of the Goblin King with Moria Orcs.

Oh and also What hero/heroes would you recommend for a Mordor army size around lets say 700 points to 1000 points

For Mordor I'm fond of the Witch-King (with the Crown of Morgul) and a couple of captains, though Shagrat the War Leader and Gothmog are very popular choices.

_________________
"...in the end the Shadow was only a small and passing thing: there was light and high beauty for ever beyond its reach.”