Portugal travel

This issue comes up frequently on this board: while we think of Spain and Portugal as practically one country and assume there are good transit links between them, they are quite different, and transit between them is, overall, poor. There are few train connections. You can drive, but a car rented in one country and returned in the other comes with a very high surcharge (someone recently posted €600). If you rent and return in the same country (even different cities), you can avoid this. There are flights, but some of them require connections. And there are buses, which is what most people end up using. To look at flights, use http://www.skyscanner.com/. To look at train schedules (and don't get your hopes up, because even Madrid to Granada is a long train ride), use http://reiseauskunft.bahn.de/bin/query.exe/en. I don't know which site to use for bus schedules (there are multiple companies in each country). For hotels, what is your budget, in euros?

We cannot drive. We prefer to fly. Is there a flight directly from Lisbon to Granada(or Cordoba)? Is Granada close to Cordoba? How long by train? Hotels: Our budget for a centrally located hotel (breakfast included is a big plus!) is about 200 Euros-. Any recommendations? What is important for us is to have a flexible fee (canncellation/change option) because we buy insurance and it is very expensive to cover a pre-paid hotel. Thanks!