This is the customization screen.
The weapons are modifiable. Their are 4 diffrient weapon types. Direct (Rifles, autocannons, long range bunker guns, machineguns, and a shotgun), indirect (Mortars, either guided and unguided, grenade launchers, grenades in 4 diffrient flavors (Standard, heavy, self destruct (pretty much a satchel charge/super heavy grenade) and EMP) and a couple of smaller anti-infantry mortars.), energy (Lasers in standard and higher powered pulse varients, railguns, particle accelerators (Pretty much a EMP gun) a gatling laser, a long range sniper laser, and surprisingly the few hand-to-hand weapons in the game) and lastly, my favorite, missiles (which of course includes a varity of mounted missile launchers, avaliable in a varity of strengths and a choice of payloads (Either standard explosives or incendiary), bazookas, a special rapid fire bazooka, and some some jury-rigged hand-held missile launchers)
As for the mech itself, you choose it before you get to the customization screen but their are 4 diffrient classes (Light, Medium, Heavy, and Assault) L/H/A have special Dark versions of other gears, which are pretty much a much stronger version of its base type. (Cheetah (L), Jaguar (H), Mamba (H), Warrior (H), Cobra, (A) and Kodiak (A) are the dark versions. Warrior is kind of strange though, since it breaks the pattern of dark versions being stronger versions of a base model. Warriors are Medium class, but the dark version is classified as a heavy. The others follow this pattern though.) You can modify the mechs stats too so the only real diffrience is the design between a class. (The class determines the amount that you can raise speed and armor though. But this still lets a Light unit get the armor to match a basic heavy, not to mention the additional speed that lets it dance around stronger units which they usually do even at base speed.)
Back to the weapons though. You can change the point where most of them are mounted, although some can only be mounted in one section or only support a couple of mount locations. The mechs all have the same amount of mount points though. (1 back, 2 collar, 2 shoulder, 2 hip anything else for handheld) The mechs only support 6 weapons max though so not all points get used.
As for the perks and flaws, manipulable arms are standard. I'm not going to get into what perks are better because it depends on the person, but I will say that Zero-G and Submersiable are not needed unless you are playing on a space map, or a map with lots of water. Flaws weaken your mech and reduce its threat ranking but yeah... I'm not going to argue about what flaws are better because really, whats the point in having the better weakness?
The part under the threat ranking shows the current varient of chassis you are using. Most have a couple of varients other then standard, but you can make additional varients. (A varient is pretty much your perks, weapons, and stats)