Dave,
I am not an expert and sports medicine is not my line of business. I can only share by what I have learned as a runner and hiker over the years. Also, I need to be careful that I do not offend anyone. If I do, it is not my intent.
But lets look at the two problems; knee pain and shin splints (if that is what is happening).
Starting with shin splints. Often this is caused by over-exercising or over-use of the muscles. Also can be caused by stretching your muscles if you over-pronate. Worse case is stress fractures; this happened to my son after his sophomore year in high school when he upped his mileage too fast and too intensely.
So if we start an exercise program, we need to start with our general physical fitness. If we are over 30, a physical examination and general discussion with a doctor might be in order. Guilty… I have never done this; I only go to the doctor if I need something like a gall bladder removed.
If we are overweight, our skeletal structure may not be conducive to running… yet. We need to slowly and carefully change our diet and start a very light exercise program. Easy walking is great as are some aerobic or gym exercises. We really shouldn't start running until we get down to a reasonable weight. Then the running needs to be very light, only a couple times a week. Best to run on grass in a park or similar. A little barefoot wouldn't hurt, but I am not necessarily advocating that. Shoes should be flat. No heel lift. No motion control. If one has never run much before, some sort of minimal shoe will you help learn a natural stride. But remember we are only doing light running on soft surfaces.
And from there you slowly increase mileage. If you read some of the threads here on 5-fingers and similar footwear; most users will tell you that running in them caused new soreness… mostly in the calves, as their stride changed to a front foot strike. All of this takes months. Too often we are "couch potatoes" and then we jump up and go for the glory. Don't run on cement or asphalt… at least until you have gotten into reasonably good running shape, and then it sill might not be a good idea. Cement or asphalt does not bother me… unless I have not run in a while.
It is estimated that over 50% of people over-pronate. At lot of this has to do with weight for many people. The legs and muscles were not designed to run with the extra weight many of us carry. Lets say that we weighed around 180 lbs when we were 18 years old and at that time we were in fairly good shape; and today at age 40 we weigh 220 lbs. We need to seriously think about losing 30 or 40 pounds before we get to a strenuous exercise program. That alone will take most people at least a year to do, and it is not easy!!
The other thing is that many people do not know how to do; is run naturally… they fight their bodies, and this is where a little barefoot running at first can help.
Knees: unless there is some sort of knee problem or damage, the previous stuff probably applies. Remember I am not an expert.
Once we are in good shape and are hitting the trails or going cross country, I feel that most people should get a shoe with a rock plate. Something to protect the bottom of your feet from impact injuries. I learned my lesson on this last year. I had been doing a lot of hiking and running in very minimal shoes, the lightest that could be bought. I really knew better, but I had convinced myself that the light shoes would send a signal to my brain quick enough to adjust. Last year at about 6 miles into a 60 mile hike I experienced a pretty significant impact injury to the front of my foot. I was able to complete my hike, but I learned my lesson.
Okay, all of this sounds impractical. Take a year to get into shape. Then stay on a regular exercise plan. It takes time. But if we get crazy and rush into things, we can suffer injuries that can limit us for the rest of our hiking lives.
Regarding shoes. The shoe industry created the demand for all this stuff to help us "run correctly." Pretty much did not exist before 1970. And I think that often they have done more damage than good.
What do I use? First let me share something. I have never thought about how I walk or run, stride-wise. I just run or hike. I have a friend of who is an engineer. We have done a few hikes together and he is fairly new at it. Being new to hiking and being an engineer, he analyses everything. How often you should drink, how much you should drink, how long your stride should be going uphill and then downhill, etc. etc. Things I have never even thought about. Last year I went on a fairly strenuous hike with him, and for about 5 miles he hiked behind me and completely analyzed how I hike. I didn't realize he was doing this. When we took a rest break, he mentioned that I hike mostly on the balls of my feet. I didn't know that. But I guess it makes sense… I never wear out the heels of my dress shoes, but need to replace the soles quite often as they wear out under the ball of my feet.
My favorite shoe is a Salomon XA Pro 3D Ultra. Size 12. I wear size 10 1/2 dress shoe. These shoes fit well, are plenty big in the front, protect the bottom of my feet, and I never get a blister. They are in the stable shoe category (between neutral and motion control). I never even checked, they fit best at the time. I run in a performance neutral shoe. My next hiking shoe will probably be a more neutral Salomon, like the XT Wings or XA Comp 5.
Hope this helps. Remember, it is just my opinion.