Looking at the weapon design from a different perspective, I find the ammunition frequency and employment interesting. Let me know if these numbers seem correct to you.
.38 is the most common but is only natively chambered in one weapon class (pipe) There are however two other weapon types that can be downgraded(?) to .38.
10mm is very common but is also only natively chambered in one weapon class (10mm pistol) Can anything else be chambered for it? The Deliverer keeps the 10mm relevant but only if you join the faction that gives you that pistol.
Fusion Cells are the 2nd or 3rd most common type and are used by both Laser and Institute weapons, Lasers being common from Gunners and some mutants/raiders while institute Synth pop up most everywhere. It is the staple ammo and weapon type due to how well the damage scales and the availability of weapons and cells.
.45 is the first of what i'd consider uncommon ammunition types even though it is natively chambered in three weapon classes (pipe revolvers, submachine guns and combat rifles) Is anything else upgrade/down-gradable to .45? by the time you have enough to consider using it in a primary weapon two of those are obsolete though. Has anyone found a use for non legendary pipe revolvers or submachine guns?
.308 starts to get a little rarer but not much more so than .45. Two native weapons (bolt action pipe and hunting rifle) with one more that can be adapted to it. There are no full auto options in .308 so the rarity isn't much of a problem.
5.56mm is rare and only available in one weapon type natively and no other through modifications. This seems odd considering it is extremely common IRL and in Fallout 3 where even Chinese weapons were chambered in it to take advantage of the massive stockpiles available in the US.
.50 is rare and only used by specifically modified hunting rifles. the availability seems right though since it is fairly exclusively limited to sniper weapons.
Plasma Charges are rare and only used in the Plasma weapon class, somewhat hard to find and expensive to buy and they can be burned through quite quickly, a specific game choice to make it a very late game option perhaps? damage is great when using them in close to mid range encounters.
2mm is exclusive to the Gauss Rifle, is possibly the rarest ammo type for regularly occuring weapons but the weapon itself is fairly locked into being a slow firing sniper weapon for use on hard targets so availability doesnt actually feel that bad.
Flamer Fuel, Mini Nukes, Missiles (actually rockets but whatever) are all rare but that is not surprising considering those are the "heavies" 5mm somewhat falls into this too as it is exclusive to a heavy weapon and burns through so quickly.
My take away from it all is that the expected course for a player is to start with .38s, possibly upgrade to .45 for a short while and then regularly roll with a Fusion Cell weapon except in specific circumstances where you break out a specialist weapon.
It is strange that some ammo types are so locked down to weapon types. 10mm would be nice to see in a dedicated submachine gun again or a carbine of some kind. Who doesnt have huge stockpiles of it going to waste.
5.56mm would be ideal in a light rifle of some kind too. honestly it should have been the primary chambering for the combat rifle with .308 still being the upgrade. Something with a native short burst receiver that did higher damage per shot compared to other auto guns.
.38 doesnt really have a purpose past levels 15-20 unless you want to deck out all of your settlers with full auto pipe machine guns (an entirely feasible idea if you wanted to up-arm your settlements)
.45 would have been a nice upgrade option for the 10mm.
So yeah, the 10mm, .45 and 5.56mm are all in a kind of weird place in the game while the rest of the ammunition types/weapon classes make pretty good sense to me. i was a little surprised by the common nature of laser weapons but it fits the higher tech level available around the Commonwealth.