1. I'd go with a forest, or more specifically I'd build it on the border between a large forest and some grasslands.
2. Manticore's, good combat ability, wings allow for flight (most likely, why else have them?). Dragons and Hydras would be better for defense, but just to big to feed and control properly. Second choice, Timber Wolves.
3. Start with a focus on building and strengthening a defensible city at the edge of the forest, clearing an area just inside and using the timber to build with, followed by using EP and uni magic to grow a wall of giant trees around the city for defense, leaving only a few guard-able and seal-able passages. Use the plains for farming as well as secondary structures. once a solid base is set up and food supply is stable devote majority into research, science, medicine, magic, anything that could make life easier, better, longer, more enjoyable.
Integrate the tribes by making them all work together on any projects, while at the same time having each tribe be the one overall in charge of certain areas. EP's in charge of food, Pegasi weather (duh) and defense, Uni's head up the research groups, etc... But have all ponies spend time helping out with every task, so they all see how vital every job is to the overall welfare of the city. As well as have a thorough understanding of how everything works, so in an emergency any pony is ready to fill in anywhere that's needed. Also organize friendly contests and tournaments often, ensure there are a wide enough variety of events that just about every pony has an event they could compete well in, and encourage any ponies that have disagreements to settle them with a friendly contest of some type.
Build a fool proof system, and the world will create a better fool.