From a character's in-universe perspective (and prior to the Wars of Reaving), the Mercer beats the Lion in pretty much every category. It has more armor, more weapons, faster thrust - the smaller carrying capacity is something that would be looked at in a bid meaning that a larger complement of ground forces aren't necessary.
From a player's perspective, I'd go with the Lion-C. It provides a more diverse array of combatants and has enough room for it to be modified to carry more (also, the Lion-C carries a binary of 'mechs and a pbi binary). IGNORE THE FOLLOWING IF YOU DON'T WANT TO MOD I would seriously consider turning the binary into a Supernova Trinary with the fifth point of each star being an aerospace binary, this decreases the overall cargo capacity of the Lion-C by about 1300 tons, still leaving about 1400, more than 2.5 times that of the Mercer. This provides you with a force of 12 'mechs, 6 ASF, and 15 points of elementals, pretty balanced as far as I am concerned - and if you want some vehicles, 'downgrade' the 4th point of each star into a point of vehicles, this would decrease your overall cargo capacity by 150 tons (to about 1250) if you use only large vehicular bays, or less if you use some small ones (this version nets you 9 'mechs, 6 ASF, 6 Vehicles, 15 points of BA).
