Could at least a single barraks be added instead of a transporter? I checked the shiplist with ship edit and a few of these HDWs will have a hard time maintaining an attack using marines with the realitivly small complements on board.
romulan( SBH1): 20 marines max / 6 trans = 3 full attacks + 2 extra.
federation(HDW1): 16 marines max / 6 trans = 2(!) attacks + 4 extra.
klingon(HF5C1): 24 marines max / 6 trans = 4 attacks.
ISC (HDDC-1): 24 marines max / 6 trans = 4 attacks.
Mirak (HDW1): 20 marines max / 6 trans = 3 attacks + 2 extra.
Gorn (HBD1): 24 marines max / 5 trans = 4 attacks + 4 extra.
Lyran (HDW-1): 20 marines max / 6 trans = 3 attacks + 2 extra.
Lyran (JPG): 20 marines max + 20 marines max (barrack for the M refit) / 7 trans = 5 attacks + 5 extra.
Hydran (HDW1): 24 marines max / 6 trans = 4 attacks.
Hydran (LNH1): 24 marines max / 6 trans = 4 attacks.
I may not be an ace pilot around here but I have learned a few simple things concerning small ships, which I fly. Firstly, the marine complements on small ships are somewhat small. Because of this, larger ships can easily capture a small ship in only a few turns. The first step in preventing this is to always carry as many marines as possible on small ships. The second is not to waste them in H&R that MAY work but will GUARENTEE that you can easily be captured, due to the larger ship's capacity in both marines and transporters; Marines are precious, and cannot be wasted frivolously. When flying the Federation's HDW series, the three transporters are sufficient for small time H&R. However, with only 16 marines every attack weakens your own complement quickly. I usually avoid the marine varient because the mere 2 transporters make it highly unsuitable for any H&R action, as is usually the case with federation small ships.
Now to be fair, Federation starships (and generally all the starships that can be seen as 'bad' at H&R here) are usually unsuitable for serious H&R/capture actions as a whole, but as you have said before, "as long as it's legal there's nothing wrong with cheese."
By observing how you're juggling systems, there are 4 NWO's in HDW's; One shuttle, one lab, one tractor and one transporter. take the shuttlebay, lab and tractor and install transporters; Can a barracks be added with two transporters instead of three transporters? I am unsure what a barracks can replace and how 'large' it is.
If this is possible, I would suggest that all ships with only three marine attacks available to them be given at least one barrack in exchange for whatever needs to be sacrificed to get it; If the ship is to revolve around H&R, it should be able to do H&R without dropping any more of their pant-equivalents as necessary.
Ok? Complications? Utter crap?
Using marines would be... strange,
Holocat.
annendum: I think that captures between players don't work. To nip that in the bud, AI captures work well enough and there have been aggrements that someone that is about to be captured blow up, or so I hear. If the player vs. player ever does work, however, this is something to be taken into consideration, and should be for player vs. AI or AI vs AI battles. Additionally, the opinions above DO relate well to H&R, a fairly easy task if one dosen't have alot of marines onboard to oppose them.