I'm generally of the opposite opinion.
Because if we're to assume the typical "line" ships in Trek are capable of devastating assaults on a planetary or space station target, as is sometimes implied or shown, then burying the bridge deeper in the hull isn't going to give you much additional protection if your shields and other defenses are disabled.
That's true of anything that doesn't have Shields/Defenses Enabled or the enemy finds a way to bypass said Shields/Defenses.
You could argue that it's more dangerous to have nacelles as separate, exposed components than the bridge because if those are crippled, then your ship can't escape and can't provide power to its other essential systems. There's an engineering logic behind this of course (the nacelles were originally treated as being the source of the warp reaction, and were thus safer for the crew if they were isolated from the other components), but we've also seen many ships over the years that don't use separate nacelles to mount engines.
But that wasn't the case as we found out in TNG, but in the 32nd Century with Floating Nacelles & Miniaturized Warp Cores, I can see the argument where each Floating Nacelles has it's own Mini Warp Core inside.
That gives it superior Power Generation since each Warp Nacelle has it's own Reactor for independent FTL Propulsion & Shields.
The rest of the vessel, the Saucer & StarDrive can have independent Warp Cores.
Ergo a standard 32nd Century StarFleet Vessel would have Quadruple Warp Cores or more with at least:
Saucer = 1x Warp Core + 1x Impulse Reactor/Engine set
StarDrive = 1x Warp Core + 1x Impulse Reactor/Engine set
Each Warp Nacelle = Individual Warp Core + Impulse Reactor/Engine set
That could easily explain the power difference moving into the 32nd Century Future.
I view it mainly as a trade off with both advantages and disadvantages, and I likewise think having a more accessible bridge module has advantages for technology swaps and refits.
But you would do Bridge Module Swaps only at a StarBase or Orbital ShipYard, which you have access to Industrial Sized Transporters anyways.
So you can just beam the Bridge Module into the central area designed for it and have it be more protected by being in the center.
It's not solely a weakness when the rest of the design is taken into account. Also, the hero ships are more likely to have additional plot armor.
Hero Ships almost always have Plot armor, that is the nature of fiction.
It still is a weakness, we even saw it on ST:ENT in a alternate timeline when the NX-01 Enterprise had the Bridge destroyed.
If I was playing ST Bridge Commander, I'd always target either the Warp Core, Bridge, or Sensors.
Then finish off the enemy.
