Deciding the route of a trip is easy for some people and hard for others. It is something really personal and that depends on your goals, tastes, past experience, perspectives and, of course, time and money. Here you have some tips that help us to decide our route for this (and other) trips:
#1 - Define the number of days you have and when it suits you better
This sounds basic, but some people tend to start thinking about EVERYTHING at the same time when the subjects are holidays or trips. Calm down, breathe slowly (I know it is hard when you are too excited thinking about days off from work and thinking about all things you can do each 24h of your holidays period). What you need is to do it step by step and you will see that you will have more time to plan and organize well your trip. One of the first things you should have in mind is how many days you have and when. Do you have just one week in July? Or you can get three weeks off in October? This information will help you (a lot!) to define the best places to visit. Websites like TheBestTimeToVisit or BestTimeToGo can help you to define the countries/regions you should visit in your selected month. And the time available you have will help you to define if that place deserves the visit or not. Except for work, I think I will never plan a trip from Portugal to Australia for less than 3 weeks (the flight time and the cost do not seem to compensate in my opinion).
#2 - Plan ahead
Planning ahead means less stress, best seats/stays and less money. It is a simple rule. Maybe you were lucky once in last minute reservations, but the general rule is that you benefit more for less money if you organize and book your trip with some months in advance. We started to plan this trip about 3 months before and 2 months before we had already booked the flights from Lisbon to Rio de Janeiro and booked a place to stay for the first week. But this is even more important when you are doing a shorter trip because you have each day planned for something and you will be less flexible to change places and timings.
#3 - Define what you DO NOT want to do in you holidays
Travelling is always a personal experience and for each person holidays and travelling mean a different thing. I met a couple that holidays meant staying in the same beach for two weeks with everything booked ahead (including chairs in the beach). But I met another couple that their own rule was never to repeat a city during their trips. And there is nothing wrong with that, you just have to know what you want in your holidays. In the end, it is your time and money and only you can define what is relevant or important. And sometimes it is easier to define what you don't want.
#4 - Be honest with yourself and your capacities
Not everyone is able (or wants) to jump from a plane in the middle of the Sahara desert or walk 50 km in a day to see the Everest mountain. It's good to surprise yourself and try to do different things and experience new adventures. But do it because YOU WANT and not because everyone does it or because a book tells you that you should try. I think you should always try to do things that scare you but not things that make you unhappy or too uncomfortable.
#5 - Take into account your budget
The money is also a factor to consider while choosing the route and the places you want to visit. It is not the main factor but it is important. Before the trip, analyze the average costs of staying in an hotel/hostel/b&b, average prices of restaurants and supermarkets and the transportation costs. Also, how much it costs will depend a lot on the months you are traveling. If you are doing a budget trip, plan even more in advance, choose low-season periods, look for accommodation in hostels or coachsurfing, find cheap restaurants and supermarkets around. If you see that you do not have enough money even considering the factors I told before, look for another destination or wait a few more months to save more money for the trip.
#6 - Find the best relationship between time traveling to certain places and time enjoying that places
Don't try to see all towns and villages in a trip of 2 weeks to Mozambique. You will be the typical tourist running all over the historical attractions for the pleasure of doing "check" and saying you were there. But that will not make you enjoy any place because you need time for that. If you just have 2 weeks to visit Mozambique, maybe you can plan to visit Maputo, Inhaca, Bilene, Tofo and the Kruger Park, but don't try to go to Beira or Nampula just because you want to see all the country. You will spend more time traveling between places than enjoying them. And staying for a while means you can meet new people, relax like a local and find places that even the guide didn't referred.