I have been coaching 14/15-year-old boys for 30 years, and my perspective on this is as follows:
1. do not specialise too soon - 13 is way too young to be doing event specific training, and is a little early for "training" in the off season. have them doing games of various sorts, going for runs if they enjoy that, and having practice meets and friendly races against their peers but they should be encouraged to try a wide range of events and should be doing at least one event from each event group (sprints, middle distance, hurdles, jumps, throws). so that even if the guy is absolutely convinced he wants to be a pole vaulter, at 13 he should be doing some hurdles practice, throwing something, doing sprints, and going on 2 - 3 mile runs with the middle distance guys.
Jessica Ennis went along to a group run along these lines because her friend wanted to do the long jump but didn't want to go alone. so Jessica ended up trying all the events and ended up being Olympic heptathlon champion. Bruce Jenner went along to a similar group and ended up being a woman, so I'm making no promises, but there is no evidence that throwing the discus makes you gay.
2. progress is not linear - not even superstar athletes improve every year. just because he has shown no real improvement this year does not mean his training has not been beneficial. 13 - 16 is a really stressful period and they have to accommodate changes not only in their biology, physiology and chemistry but also in their real life, they are struggling with their identity and where they fit into the big scheme of things, they have to figure out what to do with their lives and to resist a lot of temptations being thrown their way; things like drugs, girls, alcohol, girls, smoking, girls. their body is, essentially, a war zone, and adapting to any of this in ways that improve running performance is not a priority and is highly unlikely.
concentrate on enjoying play, being healthy, sleeping well, eating varied and nutritious foods. get through puberty without tearing your achilles or hamstring and you're set for eight years of gradually increasing serious training.
a 13-year-old boy who even knows what his 5000m pr is, is taking it way too seriously.
3. boys respond to puberty differently - some boys, their voice breaks and they sprout facial hair, others you wouldn't notice unless you really know them. they also start at different times, proceed at different rates and, from many years of experience, some never quite finish; they're still kids in their 30s. try not to judge your son against his peers, and, in particular, do not compare him to your memory of yourself at that age. he ain't you. he is a unique individual and stuff will happen in its own sweet time. just be there for him and everything will, mostly, work out fine.
cheers.