I think the crux of the complaint, one that I have not seen voiced, is that the ships were destroyed and not replaced.
Everything after this quote, I pretty much agree with. I agree with this quote (and the complaint as well), but from the completely opposite end. Battletech needs obsolescence badly. It needs things to go away and never come back. It needs new things to replace those missing things. There's a reason that TROs are one of the top sellers. Unfortunately, the mentality behind WarShips (that of obsolescence to eventually be replaced predominately by carrier DropShips and pocket WarShips) hasn't been applied to the rest of Battletech. Most non-naval, non-infantry unit types are pretty bloated with designs. New designs don't seek to fill missing gaps, because there's still hundreds or thousands of the old things floating around. Extinction isn't a threat for most unit types (particularly 'Mechs), and that leads to the situation you have now.
Let's go with an example (and something that will likely be viewed as sacrilege). When the Phoenix designs were lost (the visual aspects of them, that is), they had an amazing opportunity to give a whole new generation of units a push. How awesome would the Hammerhands have been, if it became the entire replacement for Davion Warhammers? How much less boring would the Warlord be if the Davions had said "We can't do BattleMasters anymore, and we need something to fill that role. Here you go." Project Phoenix was something that hamstrung the future development of the game in the worst way. Two TROs later, we're already getting another entire Phoenix section. We keep going back to the same old designs, which makes the new designs seem pretty superfluous. It's led to a growing sense of bloat and blandness among these combat arms.
Now, the one place that hasn't happened in BT? Naval warfare. You actually have a clean break, and a clear point of obsolescence in the Jihad. Going forward, the factions realize that they need something in that role, hence the expansion of pocket WarShips and carrier fleets. Have you lost the big battlebarges? Sure. But here's the interesting question...when did you ever really have them? They weren't around at BT's creation. They weren't given stats until Battlespace. But considering the current era being written at the time of Battlespace (leading into the Clan Invasion and forward), when did players suddenly rush out to begin playing large naval actions? They didn't see use during the Clan Invasion, until the Twilight of the Clans (and then in two or three limited conflicts). They saw a few limited conflicts during the FCCW. So where was this giant fleet action era in any of the actual timeline of written Battletech material? Way back in the Star League, in an era (that up to the pre-Jihad writing period) had exactly one out of print book covering it? On their home table top, maybe. But now you are asking Battletech to support your own non-canon play with canon product, simply because you want it that way.
That means that the massive fan outrage about WarShips isn't exactly so massive. In over 25 years of selling product, Battletech's creators have never found an overwhelming market for products relating to WarShips or the era of massive naval conflicts. Sure, the outrage is vocal online...in a tiny, tiny, nowhere near representative minority of the Battletech customer base. But sales numbers don't lie. TROs sell well, so new toys clearly sell. And of those new toys, 'Mechs sell. What hasn't sold? WarShips, judging by their less and less frequent appearance in TROs, in era where their production was increasing. And here is where I find the overly vocal WarShip crowd to be a mite bit hypocritical. Under the aegis of the late-era CGL line developers (Randall and Herb primarily), you have had more product supporting large naval actions and WarShips that at any other point in BT's publication history. You have even been given material to support the era of massive naval fleets (the Star League and Reunification War era). So..what more do you really expect in the way of support for a unit type that clearly has not been a big sales driver for the overall Battletech consumer base? Honestly...of anything in the BT setting, WarShip fans seem to have the least to complain about. You haven't been drowned in unit bloat. You've been given a massive blaze of glory exit. You have a future in smaller and more varied, versatile, and interesting ship types. You've been given historical information to cover the era with the most relevance to that unit type. What the hell is missing? I'd kill to have just 'Mechs (let alone the other combat arms) treated with the same care and foresight.
