Hmm, I don't see my post. Attempt #2:
You haven't addressed the arbitrary limit on the number of crews, as well
You're arguing AGAINST the game mechanics itself, I.E. you don't have a real point. Game mechanics are made to enforce gameplay balance and to create strategic elements. Because of this, "arbritary limits" are anything BUT arbritrary. They set the scale of the game and its pace.
Sins doesn't have caps that raise with the empire's size. However, the caps that are in place exist ACROSS THE BOARD. Saying something won't work because there's a cap in one place is stupid. The hard limits are everywhere, so what really matters is that all the limits are in balance.
The most potent argument against the idea is thus:
But then I can't max everything everywhere to the max.
Which is exactly what I think NEEDS to happen with starbases. A loaded starbase needs to stand out as a UNIQUE and POTENT obstacle to attackers. If potent starbases are allowed everywhere, planet cracking is going to be a turtle nightmare. If the fix is to make them expensive, then they won't be cost effective. Starbases NEED to be cost effective, because defensive units do not make the killing blows that end games. They're also vulnerable to mobility and are inflexible to countering strategies, more reason they can't be expensive.
If you want a massive, fleet crushing superweapon armed starbase, then you need a real restriction on how they get used. Making them expensive just ruins them. Making them take up fleet supply ruins your fleet, thus taking away from the major point of "Entrenchment"-- letting you hold your home while fighting abroad. However, given a REAL STRATEGIC match going on, capital ship crews are ALWAYS in ample supply. Players rarely research cap ships to max, or even close. There is little viable reason to max out your capital ships, and doing so is a great way to get crushed against real living players.
So why not put them to use? Starbases are massive military complexes. They may be self sustaining on supplies thanks to their immobility and long term construction, but there's no way in hell you're going to leave the most important bases in the empire in the hands of a goddam junior lieutenant. Maybe you'd leave him on the dipsy trade outpost in the middle of pirate asteroid nowhere. But the Holy Death Fortress of Chamya Prime demands a REAL command crew, just as a capital ship would.
What this means is that players are left with an option. Sure, they can get the generic starbase outpost for all their systems, the kind to ward off fledgling fleets and pirates. However, the monster bases capable of crushing fleets are sacred and limited, and thus must be carefully located for the maximum benefit. All this, using the existing cap ship slots that- given a proper game- rarely sees its limit due to necessity of frigates in building fleets.
(side note- you still have plenty of TACTICAL slots to turn any system into a danger zone, even with a small starbase. You don't need monster starbases everywhere, only at the most important points. All the more reason to make them special and unique!)
On the plus side, the limit on the big starbases means that they can be FAR more cost effective without drastically altering the game's balance. They can't be spammed without appropriate research, which sets a PACE on building them(pace is vital for balance!). All this is good news for starbases and for making defenses both viable and strategic.
On big maps, there will be a point where players have to decide between capital ships or more giant starbases. The power of a capital ship will have to be weighed against the power of a high powered starbase. Players will decide if they want the fleet versatility of a cap, or the home holding power of further starbase upgrades. I think this is better and simpler than having two independant limits, which would be an extra gameplay element that wouldn't add any strategy of substance.