I like the company structure, and feel that Martian has some good choices...but I disagree on some of the replacements.
For instance, I would replace the Atlas with just about any other assault. In-universe, they are primarily Davion, Kurita, or Lyran machines while the FWL has never produced them. I am sure they have them, but if you want a faction-flavorful company to be seen as such by an average opponent, I would replace it with either a Battlemaster, as suggested, or even a Cyclops or BNC-3M Banshee . We have canon examples of FWLM forces using the former, while the latter is underated to a large degree.
The Centurion sees large use in Marik-based organizations. For instance, a classic Regulan Hussar fire lance utilizes two Archers, a Trebuchet, and a Centurion (or swap out two TBTs for a single ARC). The Capellan Confederation also uses an inordinate number of CN9s, and the Lyran Commonwealth has a very effective variation (the CN9-AL)--though I do agree that when people see a Centurion, they often think "AFFS" first and foremost.
I do not have a problem with the GTL as a FWLM design (which it very much is), but my grognardism makes me yearn for a non-Star League design in this timeframe, irrespective of the 90s-era TRO 3025. While not as devastating as Guillotine, one could always choose a Quickdraw or Rifleman, let alone a Warhammer or Marauder, in a fire lance.
I would never, ever, replace a WVR-6M with a stock WVR-6R if I had the choice, let alone in a FWLM unit. And I do not have a problem with two of them--more's the better in my estimation. I really like the Cronus, but its date of production precludes it being in a 3025-era company. And the Dervish, while used by everybody in this timeframe, is again a more Lyran or Federated Suns design; try a Quickdraw if you don't already have one. Less LRMs on-target, but more concentrated short-ranged firepower if you use the right variant. I actually like the inclusion of the HBK here, but do not forget to look into variants that swap out the meatcannon for a longer-ranged and more diversified weapons suite.
For the Sentinel (see GTL comments above as well) or Clint, I'd take either a Hermes II for flavor, or a Phoenix Hawk for overall effectiveness (or an Assassin, which was heavily used by the FWLM per the original 3025). But I like the nod to the Hermes and its bigger III brother, which are underused and are nice changes of pace from the basically lackluster stock variant. Again, we have canon Regulan forces using FS9s, but I agree they are seldom considered a "Marik" design by the general populace.
So, I'd suggest:
Command Lance
BLR-1G Battlemaster or CP-10-Z Cyclops or BNC-3M Banshee
AWS-8Q Awesome
STK-3R Stalker
ON1-K Orion
Heavy/Fire Lance
ARC-2R Archer or WHM-6R Warhammer or MAD-3MMarauder
TBT-5N (or J) Trebuchet
CN9-A Centurion
HBK-4G Hunchback or RFL-3N Rifleman
Strike Lance
QKD-4H Quickdraw
WVR-6M Wolverine
GRF-1N Griffin
HER-4K Hermes III
Recon Lance
PXH-1 Phoenix Hawk or ASN-21 Assassin
CDA-3C Cicada
HER-2S Hermes II
HER-2M Hermes
What I like is the inclusion of 16 'mechs. Plus it out to 18 or 20, and you can comfortably represent a battalion at a company level in a campaign, having a distinctly different company-structure each game. For light 'Mechs, I would suggest the omnipresent 'bug' 'Mechs as well Fleas. That way you can represent a heavy, medium, or light company with the designs you have on hand...