I kind of agree on the commando ships being unfit for purpose.
In our LAN games here, both sides tend to opt for small troop ships, which have more transporters and can have a 4 x shuttle bay ducktail welded on the tail plus a skid, under the belly, for additional stuff.
Troop Ships are listed, as standard, under "All Races" as X-FTS and X-FTL in the SFBSPC13.TXT and SHIPLIST.TXT files right at the top, but with no model assigned, for use in scenario scripts. However Taldren never used them actually in the SFC games.
Apart from being slow, troopships can land troops, carry several shuttles and even have facilities for MRS shuttles.
If I was a Rommie player wishing to capture something, and given the choice between a R-COH and R-FTS or R-FTL, I'd go for a troopship with ducktail and skids everytime, a couple of MRS shuttles, a cargo bay full of heavy weapons and other useful millitary hardware.