The Battleships I have seen have less protection. The Barge is not a battleship, except it is in more or less every way. The Idea that it needs speed and all that protection..means it is not meant to be a battleship. If you want heavily protected, you do not have speed, if you want speed you need to give up protection.
You are correct in that it isn't a Battleship - else it would be called that way, and would have more impressive firepower. The Space Marine Battle Barge is basically a heavily armed and armoured transport, its chief purpose to ferry a Space Marine strike force to their destination and support their landing by taking out orbital defences or pushing through a blockade. Its stats reflect this purpose. It still is at a disadvantage in a classic naval "duel" where a Navy vessel would bombard it from out of the Marines' own weapons range.
I agree that there should be more Navy battleships that have a clear advantage beyond the weapons range, but at least the Retribution-class has …
[click for visual stat comparison]
+ better shields
+ more turrets
+ weapons batteries with superior range
+ additional dorsal lance battery
+ torpedoes with more firepower
All that whilst keeping equal speed and maneuverability, and actually having a lower point cost than the Battle Barge. Its only disadvantages in a direct comparison are the missing bombardment cannon and that it does not have any attack craft itself. That being said, since battleships rarely travel alone, I would assume that another ship could "pitch in" for this purpose, especially given the difference in point costs.
Discounting the fact they really do have the best tech (they get first pick of pretty much everything) and the best chance to find the best tech (because they ARE the best at everything, ever. Except Navigating, as far as I can tell, which is kind of odd to me.
Well … not in GW's version of the setting. There, the best tech is in possession of the Adeptus Mechanicus, which services the entire Imperium, meaning that there are a number of powerful agencies or individuals who sport comparable equipment, in particular the Inquisition.
I know that a number of licensed/outsourced products have chosen to portray it differently, which used to irritate me to no end, and here I have to agree with Hunterindarkness in that this focus just seems a bit "out of line" with the rest of the setting to me. Sure, it works as long as you look only at the Space Marines, but tends to break apart as soon as you start perceiving the Imperium as a whole. GW envisioned their setting as having some sort of balance and not turning around the Astartes alone, and a whole lot of links in the fluff depend on the Space Marines being inferior, vulnerable or subordinate somewhere. You could of course always just discard those links, like FFG did in some cases, but to me that'd be a waste of some good potential for storytelling, not to mention crossover-compatibility!
Alas, with the franchise not having a proper canon policy, we're all left to choose for ourselves which vision to follow. I for one tend to see GW's fluff as being more balanced. Although the aforementioned SM focus exists there as well, it is usually much more tamed in an attempt to make them "fit in" with the rest of their stuff rather than pushing everyone else into 2nd or 3rd row.
As for the navigating, I do recall that Marine ships are crewed by Chapter serfs, with Marines acting as commanding officers, if they're on board at all - but given a Battle Barge's role as armed transport, I could see perhaps the Marine commanding the detachment in its holds also being placed in temporary command of the ship and its human captain, for as long as they operate as one battle group?
And the Navigators are special, anyways. They're almost as far away from normal humans as the Space Marines are. Just even more creepy.
You're spot on about the boarding, though.