I'm assuming that by "big huge robots" you're talking about Gundam/Mech -style "I'm bigger than a house!" robots, as opposed to "powered-armor" a la Starship Troopers (although there's some overlap between the two).

The first thing you need to decide, is what you want the focus of your game to be. I can think of a few examples:

• Focus on in-mech interactions.

• Focus on in-person interactions.

• Alternate in-person and in-mech.

• Mixed in-person and in-mech party.

The focus drives the design. A design can still support other modes of play, but the preferred mode is going to dictate a lot of design decisions (both in your fiction, and in your system choices).

Focus on in-mech interactions

In this mode, the characters effectively are their vehicles. Stating and advancing the mecha (and mecha-like support vehicles) becomes a focus... A character's sheet is likely to include more information about their mecha than the pilot.

In this mode, you don't need to worry about power-disparities between mecha and non-mecha characters. Mecha pretty much squish anything that isn't on their level, and that's fine (because all the players have one).

Combat encounters will almost always be fights between mecha, with out-of-mecha interludes being more narrativist, or focusing on evasion.

Focus on in-person interactions

This is probably the easiest... The characters happen to be involved with mecha in some way, but most of the game-play happens when they aren't in their vehicles. Use a standard character design, with the mecha implemented as vehicles (there are plenty of examples of this sort of setup around).

Mecha segments are kept sufficiently short and infrequent that non-mecha characters don't feel too sidelined.

Again, you don't need to focus too much on mecha/non-mecha interactions. Mecha are bad news when you aren't in one, but most combat encounters will be built around the characters outside of their vehicles.

Alternate in-person and in-mech

This is the synthesis of the above two scenarios. It'll lead to a bulky system because you need a fully fleshed out "human" set of stats, and a set of "mecha" stats.

It still operates on the assumption that all of the players will have access to mecha (or equivalent vehicles), and that mixed-mode combats don't happen that often. Therefore the rules don't need to be quite as smooth when dealing with mixed mecha/non-mecha combat.

Mixed in-person and in-mech party

This is where things get challenging, because you have to balance characters that are on entirely different physical scales. Your combat system will need to be flexible enough to accommodate both at once without breaking.

To begin with, I would avoid using constant social/mechanical constraints against the use of mechas as a balancing factor. Keep them if you like the flavor, but understand that GMs and players alike will be actively looking to downplay them. If a player signs on to play a mecha, they aren't going to want to NOT be a mecha while they wait for the stars to align.

What you need to look at, is what's necessary for humans to occupy the same battlefield as mecha:

• How can humans withstand mecha-scale firepower?

  Perhaps the humans are dramatically more difficult to hit, or have a chance of "taking cover" to turn a hit into a knock down.

  Or maybe humans simply wear powered armor that gives them a relatively high degree of durability.

• How can humans approach the speed of a mecha?

  Jetpacks, flight suits, jeeps, or genre conventions can all apply here.

• How can humans harm mecha?

  Planting charges, or BFGs, perhaps?

The goal here isn't to equalize humans and mecha, but simply to get them somewhat close to each other. Close enough that a mecha does not automatically blow away a human, and that a human doesn't automatically evade a mecha.

Finally, you want to give both mecha and non-mecha characters distinct niches within combat.

Mechas are easy: They're big, strong, durable, and often fast.

Humans are harder. Perhaps humans have mobility modes not available to mechas (flying, quick turns on a grid-map, etc.). Perhaps humans can hijack opposing mechas. Or are much more accurate in their attacks. Perhaps humans are the masters of stealth (becoming the equivalent of a rogue class).

The Goal

Regardless of mode, the goal remains the same: Give all characters the ability to meaningfully interact with all major modes of play that is true to their character. Sometimes this means forcing everyone to have a mecha. Sometimes this means giving the non-mecha characters a leg-up.

Ok, first of all I'd like to say that making characters like this is one of the main reasons I role play, so I'll be trying to come at this from both sides where possible.

The first problem is the power divide.
The best way I've found of dealing with this is with making time the biggest problem.
Unless they have some way of manipulating time it is usually the most limited resource, as everything else can be gained given enough time.
If there is too much for him to handle then he will have to decide which things he wants to deal with personally and that will limit the occurrence of the problem situations of making combat encounters for everyone.

The next issue would be fame.
If he is so powerful then antagonists will start to hear about him and will start factoring him in when they plan.
You said he is taking advantage of an "Infection" in a way that it wasn't designed to be used.
A smart antagonist that knows a werewolf is coming to get him will hide during the full moon, or better yet, have wolfsbane.
Your antagonist can do interesting things like weakening, disabling, curing or more interestingly mutating your player.
This has the side benefit for a player that pays attention of showing that you are trying for them, catering to what they do so that they have a more interesting game.
The important thing is to not just surprise them with something permanently disabling as them they will just feel like they are being targeted.

If you must use rules then try to work out something works for both sides and is creative.
As you said, he's worked hard to get where he is, probably put a lot of time into a character that he really likes.
If you can, change the powerbase to something that works rather than just removing it from him. Also, do it with a story so that it doesn't break the immersion of your game.
For example have the players destroy an ancient artifact that was what was allowing all his powers to work together normally. As a side effect the powers, now in conflict within him, cause him to be luckier and so he gets a greater income or people become strangely attracted to him, causing him to have more helpers and influence in your area.

To directly answer the final question, either separate the objectives so that it is rare that he dominates and is ok when he does or create situations to bring him in line with others when it happens so that there is no divide.