You can get more loadouts by either opening cases, crafting or buying Bronze loadouts from the store.
I’ll assume you know about cases and the opening of them.
Crafting is a relatively new system that involves recycling cards into Fragments, then using Fragments and Credits (or Crafting Kits) to craft a random loadout for a merc of your choice in a rarity of your choice. Here’s the list of costs:
http://i.imgur.com/vRGzFkx.jpg
Purchasing Bronze loadouts from the store is the only guaranteed (no dice rolling) way to get a loadout. Each merc has 9 cards in Second Edition, 3 of each primary. (These are the only weapon and perk combinations available. Iron/Lead cards have the same weapons and augments, but are missing the last 1 or 2 augments. Silver, Gold and Cobalt are identical to their Bronze counterparts, except for skins.) Each card is 17,500 Credits or $3.49 (or your regional equivalent), but there is also a pack with all 9 loadouts for a merc that is 100,000 Credits or $19.99 (or your regional equivalent).
I would advise crafting Bronze Thunders. Assuming there is only a single card you want, it is an expected 9 crafting attempts to get it, which puts the expected cost at 13,500 Credits, less than that of buying it outright (17,500), with the chance of it being less or more. It would also cost Fragments, which might or might not be a problem, depending on what cards you are willing to recycle.
In regards to Thunder’s weapons, they are all usable, but the Stark is widely considered to be the best. I’d recommend the S92 (Stark, S&W, Stilnotto with Looter, Unshakeable, Drilled) as my pick of Stark Thunders and the MA42 (MK46, M9, Stilnotto with Spares, Drilled, Tough) as my pick of MK46 Thunders.