I recently posted a similar question about our DD: http://www.mamapedia.com/questions/14380953215292276737.
Our daughter is small, as was I as a baby/child. She was born at 5#13oz & at 15mo only weighs 18#. This said she is progressing, following her own curve on the growth chart (length, weight, head circumference). At each check-up she is making progress & this is key. Not so much the curve itself but the actual number of pounds & inches is gaining.
Is your son making progress, growing & gaining weight? As long you continue to see growth, doc feels that skull feels normal & he is meeting milestones then I would just suggest getting a second opinion before you go through with an MRI.
Not that your ped is wrong, each has a philosophy/experiences that shape how/why they do things. I am not a dr. & each child is different but there are few things to consider-- 1-meeting developmental milestones? 2- has skull fused over soft spot? 3- is he showing growth at each visit?
At this point, in our case, hubby & I have decided to wait on the MRI since DD is meeting all her milestones & no concerns the skull formation. We have taken DD for a 2nd opinion & continue to monitor her growth. We went back 4wks after our ped shared her concerns & had DD's head remeasured (of the 3 measurements, it is most commonly mis-measured) and she showed growth, followed-up with a second opinion which gave us peace of mind. 2nd ped checked for several things and in our case decided as long as she continues to show improvement/growth at each visit & continues meeting all milestones that we should be safe to put a hold on the MRI.
I would suggest seeking out a pediatrician for a second opinion at your nearest Children's Hospital. These docs often have better access/contacts with specialists (neurologists, geneticists, radiologists, etc) that can be helpful in viewing the whole picture.
Good luck!