I would consider myself to be a pretty serious lifter and have been for about 4 years. I put on 30 solid natural pounds of muscle in my first 12 - 18 months and the following is what I believe, just my opinions from reading and doing.
Legs are key as mentioned above, and they are neglected by most people. They are your largest muslcle group. Weight lifting tears muscle, then the body repairs these tears and hench our muscles get bigger. Lifting hard with your legs causes your body to repair this large muscle group and in doing so you burn a ton of calories long after you have left the gym. Fat middle aged women try to lose weight with cardio almost exclusively, a big mistake. Weight training, legs in particular is a fast track way to lose weight, but nobody seems to know this.
Creatine works. It's controversial, but people who bash it are usually misguided and uneducated with respect to creatine itself, and training in general. Good old fashioned (and cheap) monohydrate is the way to go. Follow the instructions for the loading phase, but DRINK LOTS OF WATER. Water is needed for training, but is also key for creatine to work, and you liver to avoid being stressed. People who say creatine hurts your liver are in early 1990's mode, they are wrong (so long as you drink around a half gallon of water or more per day). People who say creatine bloats your muscles with water are correct. But if they are suggesting that it is all fake water-weight type muscle than they are wrong. You're muscles will get bloated, when you stop using creatine they will indeed deflate. BUT, I promise you that you gained more mass and muscle than you would have otherwise. So they are half right. Creatine brings water to the muscles, aiding repair and recovery. Repairing the muscle is the point of training in the first place, it's how you grow as I said above. Your not using creatine correctly if you don't include the water!
Whey protein is good and even people WHO DON'T TRAIN could most likely benefit from having whey protein shakes every day. The avg person DOES NOT have enough protein in their diet. Therefore, someone looking to add muscle (good muscle) should absolutely add whey protein to their diet. 3 scoops per day. About 20 grams pre workout, 30 grams IMMEDIATELY after a workout and then again in between lunch and dinner if you train in the morning. Even a light trainer should have 1.5 grams of preotein per pound of body weight per dya, 2 grams for people seeking good solid mass gain. That is a lot of protein my friend, you won't get it from eggs and tuna. Protein baby, it's good, it's a must. You are doing yourself an injustice not to use it. Go for whey protein isolate if you want the real deal, worth the extra cash.
I think your cardio is good. A person looking to get fit and build muscle is best served by alternating cardio / weight training each day for six days with rest on the seventh. Weight training builds muscle which increases metabolism. Increased maetabolism burns fat, less fat means more muscle which means increased metabolism! See the cycle? That's a win win.
It sounds like your not out to get huge, but it also sounds like you need to train harder. I get lightheaded and nausious on a regular basis in the gym. Thats a good thing. I hurl about once a month, that's training hard. I also have bad bad shoulder pain, bursitis. When it flairs up I ice 3 times a day and take 800 milogram motrin three times a day to bring down swelling. Lots of work, but I get better. The key is to find a way to keep training, and to find ways to train hard.
I recommed the following for your weight training
Day 1: Chest/tri's You figure out the movements that are right for you but the meat and potatoes will be flat/incline/decline bench and fly's with dumbells. Hit both chest and tri's at the end with dips, weighted dips if you have the strenght. Tri's will be pushdowns, scull crushers etc.
Day 2 back/bi Back excersizes will be your rowing and pull downs back extensions etc, and you know what to do for bi's, curls for the girls brotha! Oh, mix in a forearm exersize too. Strong foreams will help your grip which help you in almost any excersize you do. Plus big popeye foreams with some solid veins is always a plus, and in business when you shake a hand and a person sees what you got going on in those foreams they will make a note, even if it is subconsious.
Day 3 Shoulders/legs try to get your shoulders healed and then get them stronger. Military press, shrugs, arnold flys etc, and train those legs HARD. Strong legs will increase strength and stability for your entire body enabling you to train harder, plus all of the metabolsm benefits I already mentioned. Squats, extensions, etc.
I think if you take what I said about water, creatine, and whey protein and try real hard to find a way to train harder for 4 weeks you will say holy crap, Nut from NH was right. Some real results will breed real motivation and that's how you stick to it and continue on the path.
1 more thing, when your body is right and your sholder is better work yourself the other way on your reps, that is to say go down. start doing 3 sets of 8 reps at a higher weight for everything for 4-5 weeks, then go to just 5-6 reps for 3 sets, then if your body can take it go all the way down to just 3-5 reps for 3 sets. By this time you will be throwing around serious weight, or at least to you it will seem like serious weight. You may find this kind of lifting to be completely different, and you may love it. Once I did high weight low reps I was never the same. I was the avg guy doing avg stuff with avg results. But throwing around that weight was new and fun, and clicked the primal switch. Then i LIKED going to the gym and started pushing hard.
Try it if you can, even if you just get down to 6 reps it will be a good shock to your muselces that should trigger new growth and break a plateau.
Good luck man. Keep looking to learn too. You should look for other opinions and literature to develop your own plans and opinions.