I will try to traduce a guide (pm me for engrish phrases) that I wrote using italian language, so © for me 
It is made of my personal thoughts, goals and challenges I deal with everyday to become better in fitness.
It is not technical and it's made for newbies on board.
[1] Before everything you say, why?
It helps to become immortal 
http://www.rayandterry.com/transcend/
And a lot of stuff other than health,
like intelligence, efficience in every situation, self-confidence, beauty of the body.
[2] So, what is fitness?
I think the best description of fitness is here, in this article of crossfit http://library.crossfit.com/free/pdf/CFJ-trial.pdf.
So, fitness is a concept we can divide in parts, but we can't do the same with our body. Remember the general principle of holism (Aristotle in the Metaphysics: "The whole is more than the sum of its parts"). EVERYTHING is used at the same time, and you can't isolate for ex. power and strength.
Lets analyze this categories:
-3 very different energy systems to regenerating ATPs.
ATP is a molecule you use to live and work. It's in every cell of your body, and it is regenerated every time with some process:
aerobic for long-easy work, anaerobic lattacid for quite long-hard work and anaerobic alattacid for short-explosive work)
-Nervous system improvements aka Coordination (which is the ability to move in the right space and time)
-flexibility (ability to increase Range Of Movement, ROM).
All this systems are muscle specific and ROM specific (ex. you can have strong arms and weak legs)
Everything besides that are just marvelous non-useful ideas or too specific categories.
For example:
-increase stamina? There isn't one research that demostrate the actual possibility of becoming faster in making ATPs with some specific exercise, that's not possible, they are chemical reaction that have fixed times (like 30 sec for 70% and 3 mins for 95%), you can only optimize your coordination or the involved energy system...or motivation.
-endurance? It's basically specific coordination and the use of a energy system in all its capacity.
It can be a type of training, but it doesnt corresponds to a specific process in our body (apart from using proteins and fats ex. marathoners "destroy" themselves, the body isn't make for running 42km! See http://www.arthurdevany.com/?p=1262).
For more info check Anaerobic Threshold and VO2MAX.
-Power, speed, agility, accuracy? Again, they are way of training the same thing, coordination (defined as the ability to move in the right space and time) with a certain amount of the energy systems.
-Balance? It's a sense and it can be somewhat trained (ex. gymnasts who spin and don't have headcaches), but for semplicistic reason I put it on the now enormous category of coordination
So, what an amazing body we have, didnt we?
[3] What I have to do?
Combining
Gymnastics1, Weightlifting2, Athletics2
with Swimming1, Climbing1, Martial arts2, Juggling1.
***1 is for shoulder girdle dominant, 2 for hip dominant.
Impossible? In fact you can use everything you want to improve the category I wrote in the paragraph before!
Like Coach said, "exercise is exercise. Period."
And if you can do it with your bodyweight it's quite always better, since it improves at the same time the necessary coordination for doing that specific exercise in the real world (and not just in the gym!). You will notice that gymnastics offers VARIETY, which is a great thing since some sports become boring after some time.
So, you can take exercises that are somewhat sport-specific and use them in your personal situation, some examples:
Gymnastics: HS, L-sit, V-sit, Manna, press to HS, pullups, dips, muscleups, Levers, Planche, vaulting
Weightlifting: Squat, Deadlift, Bench Press, Press, Clean, Rows
Athletics: 60m, 100m, 200m, 400m, hurdles, hammerthrowing, long jump
Swimming: all the styles for endurance or for power
Climbing: on a rope, using only your hands, for speed...
Martial arts: kicks variation of all types (taekwondo and capoeira), grappling (judo, aikido, jujitsu), striking (boxe, karate)
Juggling: with different things.
[4] Setting goals...what goals?
Ok, so now what I think it's the most important thing for a newbie is understanding my point of view, which is increase fitness in general, not in particular!
When you put yourself in this state of mind, other things will slowly come, like less bodyfat and more *** appeal.
How do you reach the state of perfection?
In fact it can never be achieved. Our body (and world) is made of infinite changes, and perfection is a static state. Like Bruce Lee said: "The sky is the limit". Try to do every time something different, to do better what you can already, to do one more repetition for your mom and one for the Marine Corps ( ) and you will always be perfect.
What you have to do? Working hard!
Howerever, trying to reach this goals in the proper order can be easier than training without a clear picture in mind, or doing something you aren't ready for.
You can start from the second block if you are in good shape:
---1st Block---
0) Over 20% bodyfat: diet. Reduce your BF to 10%. It's not so hard to eat less and better food...
1) Start doing cardio: reach 30 min (first cycling then running). Start to do some mild stretch.
2) Easy BW exercises: do pullups, pushups, squat, sit ups. Reach 10-30-50-100 rep.
The ten pullups are the more challenging, use pyramidal scheme to get it (ex. if you can do 1 pullup, do 1-1-1, if you can do 3 then 1-2-3-2-1) do the movement in all the ROM avaible and use bands if you can't do even 1; 30 pushups and 50 squat are quite easy, just pick up the max number of reps and do the 60% x 3 sets; 100 situps are a lot but they will help you with the necessary core strength.
3) Run 60 min. It's easy, just do 5 min more every workout!
Now you are in a pretty good shape. This is a fitness basic level you can reach in a year.
---2nd Block---
1) Start gymnastics training. Handstands, L-sit. Buy the rings and do muscle ups, levers.
2) Deadlift 1,75xBW, Squat 1,5xBW, Bench 1xBW, Press 0,75xBW.
3) Re-run 60min (or swim if you prefer, I'm not very good at it!) and then start working on speed (learn good technique)
This is the level of a fitness enthusiastic. 1 Year of work, more or less. You are half way to become an athlete.
---3rd Block---
1) Advance in gymnastics. Full press to handstand, V-sit and planche.
2) Decide if you want full strength or endurance. Strength: Squat 2xBW, Bench 1,5xBW, Press 1,25xBW.
Endurance: starts working on distance in swimming/running/rowling/whatdoyoulike (ex 5km, 10km, 20km)
Congrats, you are an athlete if you have completed this level...why arent you famous?
---4th and 5th Block---
I have some ideas on this level of elitary athletes, but really I'm not interested in speculate a state of being which I dindnt achieved.
This is the moment when fitness ends and sport-specific begins. View professional Olimpic Weightlifters/swimmer/whatever, and decide what you want.
I wish I had time to become a gymnast, like Coach says in his article "The Journey" its the best choice for overall fitness.
