By way of clarification, let me ask which of the three following views best represents the nature of Mecha in your game:
1) Mecha are so much a part of the theme and setting of your world that EVERY FIGHT, EVERY ENCOUNTER, EVERY MOMENT will be spent inside of a mecha.
2) Mecha are more like magical items (or vehicles) that the characters get into and out of often but combat always occurs at the same scale. When characters are in mechs, they ALWAYS fight other mechs or monsters approximating mechs (like in Power Rangers or Voltron). Likewise, when they’re not in mechs they fight normal monsters.
3) Mecha are more like magical items or vehicles that characters get into and out of. However, there will be times when normal characters will have to fight Mecha sized monsters or when the characters will have mechs and the enemies won’t.
Depending on which of these is most true for your game, will depend on how much detail you’ll have to add, how many rules you’ll have to write and how much you’ll have to worry about game balance.
FIRST STATEMENT MOST TRUE
If the first view is more true, then there is really no need to change anything except your perspective. Characters start out as mecha pilots and are assumed to always be in a mecha. The powers they gain are maneuvers they unlock, install, upgrade to, etc. Items become parts and attachments. Crossbows and bows become guns, swords become... well, they stay swords, but now they're giant MECHA-swords! You get the idea.
Going this route, all that really changes is the paradigm in which you present the rules to your players. Essentially no rule changes. The most you *may* have to do is create rules for when the characters, on those rare occasions, are acting 'outside' of a mecha- what happens when a character must eject, what happens when the mecha is destroyed, etc.
Of course, you could just RP all these encounters as skill challenges- so you wouldn't have to deal with non-mecha combat.
SECOND STATEMENT MOST TRUE
If the second view point is more true, then you're going to have to worry about the actual design of the mechs. To this end, ask yourself what's the functional difference between a character and a mech?
If you're going to keep mecha fights between like opponents then you don’t have to worry about scale because the power of the characters will always be relative to the power of the monsters. After all, if a character climbs into a mecha it's already assumed that their powers and capabilities are going to be enhanced greatly. You don't need bonuses to represent that.
That said, I would try to keep the difference basic. Make the 'mecha' just a template- a set of bonuses and extra powers that the character gets while piloting. This way, if a mecha is of a different type than the character, then you can make bonuses to represent this difference. If you climb into a tough mecha, you get a bonus to AC and Fortitude. If you climb into a speedy mecha, you gain a bonus to initiative and speed. This way the characters are still their characters, they just have different bonuses and powers (like magic items!) while in their mechs.
THIRD STATEMENT MOST TRUE
This is the hardest, most involved view point. If there’s a chance that during any combat encounter that one side of the battle does NOT have mechs, you are going to have to do a full write up for the mechs AND worry about scale.
After all, if the characters with mechs fight a band of orcs without mechs, the characters are going to slaughter them. It wouldn’t make sense for a group of level 8 orcs with spears and axes to pose a serious threat to a group of mechs, - EVEN IF THEY ARE ALSO LEVEL 8!
If this is the route you’re going for, then I agree with what FissionEssence said- represent the mechas as monsters that the characters play when inside. You’d essentially need to write up new, higher level monsters for the characters to control during ‘mecha combat.’
Hope this helps.