I wouldn't worry too much about comparing your recovery time to other people, as we are all different. Personally, my recovery varies between events for some known reasons (e.g. a hot race means I struggle for a few extra days) and some unknowns, so I always take it as it comes.
PS a very random one - I did have a friend who suffered badly from shin splints, and after various check-ups etc it was discovered her laces were too tight. Just easing them off cured a problem that plagued her for months. The likelihood of this being the cause for you may be low, but its a quick & easy thing to test.
GPs don't tend to be helpful when its not affecting your Quality of Life (NB this is a bit of a generalisation and I realise some GPs are better than others). .
It might be worth paying for a physio or sports therapist to have a look at you, and potentially identify any weaknesses in your lower body (weak glutes etc) that could contribute to this. Also have a look at Chi running or POSE(?), which look at running form. I read the Chi running book, and whilst not sold on the "philosophy" of the book etc, it did make me assess my running style and focus on some weaknesses (and I've been injury free for several years).
I'd also look at your shoes, especially if you've stuck with the same make/model, as the only time I've had continual aches and pains from running was when I had the wrong shoes (for me).
Does sound like it could be a virus or similar minor ailment, and this is the classic time to suffer from them with the change of season. Have you had any symptoms on non-running days?
If you are running 3 miles you shouldn't have to worry about hydration especially during the exercise (just think about most races where the drink stops are at least 3 miles apart, and this is under race conditions). Try cutting out the pre and during run drinks and then drinking to thirst after the run to see if it makes a difference.
The other thing to do is to slow down, if you haven't run for a while the temptation is to attempt to run at the pace that you know you were previously capable of maintaining - but it takes some time to build back up to this level.
Just some ideas from a non-medical person - as you say, if the problem persists you should seek medical advice.
I used the RW plan for my first marathon a few years ago, and just missed out on a sub 3:30 (but that wasn't the plan's fault). Just because the plans a few years old, doesn't mean its out of date as the fundamentals haven't changed in this period.
Since the fist attempt I've used Pfitzinger & Douglas upto 55 mile plan from their "Advanced Marathoning" book, which has been used by a lot of forumites.
The other option would be Hal Higdon plans that are widely used and recommended.