I think I'm about ready to call my second play through done. The Argo is fully upgraded, and I've managed to become Allied to five factions (the Restoration, Canopians, FWL, Taurians and FedSuns), and have over 51M in the bank. All (five) of my pilots are straight 10s across the board, though Medusa's pay is 1,000 C-Bills lower than the rest for some reason.
Despite actively looking for another Atlas, my 'mech load out ended up exactly where my first play through did (the Atlas II, Star League Highlander, and both variants of the 3025 Highlander). I changed the name of the unit to the "Highlancers" after I landed the third Highlander. Both 3025 Highlanders carry 55 LRM tubes and a Small Laser or two as back up. The Star League Highlander has 30 LRM tubes on top of the Gauss and 3 Small Lasers for up close work. The Atlas has two LRM-20s (with various pluses) on top of an AC/20+++ (+20 damage and stab) and a few lasers (a +10 damage Medium and a pair of Smalls). Glitch is absolute murder with Precision Attack and that AC/20. She even managed to down an almost pristine Awesome in one round that way.
The only mission objective I was never able to figure out was saving the wounded during the second Panzyr mission. When I tried it with a light, fast 'mech, it was shot to pieces, and a heavier one just can't get up the hill fast enough. That doesn't stop you from winning the overall scenario though, so I eventually just moved on.