You're correct about the Pocket Warships developed after the end of the FedCom Civil War, and after the Jihad it appears that those were preferred over Warships. But between the 2nd SW and until the end of the 4th, the logic was that Jumpships were more vital than Warships because without them interstellar nations couldn't exist, thus space combat became limited between Dropships and Aerospace Fighters (which didn't require weapons designed to engage Warships, like the Pocket Warships carried later), and Jumpships would quickly surrender rather than being destroyed since they were nearly irreplaceable and could be recaptured later.
The rediscovery of Star League technologies after the 4th SW meant that Jumpships could be mass produced again, but Warships only started being built again after the Clan invasion, as a response to their usage by the clans (which was completely different from the 1st SW since the Clans usually bid them right away during trials, unless the opponent also had Warships).
Even at their height prior to the fall of the star league the successor states didn't invest much into WarShips; the Terran Hegemony was ahead of them by leaps and bounds. In 2765, right at the start of the SL Civil War, they had 239 across the 5 of them, while the SLDF navy (essentially Hegemony) had 2,250 WarShips and about another 1,000 in mothballs. The designs also fit different doctrines. Hegemony/SLDF WarShips were built to fit specific roles in the fleet and act as part of a battlegroup while successor state ships were much more multirole and better capable of independent operations.
Once the IS economy and technical base started ramping up in the early 3000's, making WarShips wasn't a priority. They're massive investments requiring exotic technologies and extensive infrastructure to be built from scratch. Meanwhile a lot of other recovered tech was much easier to develop and ramp into production. The Clan threat caused the successor states to launch a crash program to build WarShips and then their fleets grew pretty rapidly. Then the Jihad happened and most of those expensive shipyards got WMD'd and a fair few WarShips ate nukes. Turns out that expensive strategic assets are just asking to be hit with a headhunter attack.
During the FedCom civil war/Jihad a lot of factions ran with the pocket warship (PWS) concept and you see the top size of combat dropships go from 4,500 tons to 36,000 tons. You see PWS squadrons fight and win against full size WarShips. Furthermore, brand new 'subcapital' weapons allow dropships to fight effectively at much longer ranges than before. After that war, the factions invested in PWS production. After all, PWS are far cheaper to build and a lot of them can be built dirtside. WarShips become strategic assets, centerpieces of naval battlegroups largely built of PWS. The RotS ends up building 100k ton monsters that can stand toe to toe with smaller WarShips.
Outside of the fiction, one big issue with WarShips in the game is that any fight you put them in regimental in scale. Pretty much all of them are named and accounted for. As a player, it is nearly impossible to play a game with one that fits with the lore. Meanwhile, a PWS battle can happen at far smaller scales and is much easier to pass off as a border skirmish or other small unit action common to the universe.
Sorry if it is a little off topic but I love me some BTech naval discussion.
As for stuff I'd change - I'd fill in a bit more about how and why the technological revolution kicked of as quick as it did. I think it makes sense personally, but there is precious little content that actually addresses the post-Helm renaissance. I'd also tone down clantech while also making them less stupid. Seriously, even as awesome as their stuff is they had no chance taking over the IS with just the handful of clans that invaded. If you make them less OP individually, you can have them actually attack as a cohesive group. You know, intelligently.
