So, Goldbrease, just looked over your profile in full...
Well... what's to say...
One, I'd suggest you nix the Shadow System. Mecha, especially yours, tends to be powerful enough that the fact that radar/sensors can pick them up from beyond the horizon is about the only weakness they have.
Mostly, the history. It'd help out if you pointed out which parts were actually roleplayed out somewhere or not. Most of it seemed quite, off. What I mean is the manner it's written in is like watching someone with no experience drive a stick shift. Start, stop, start, stop, start, stop. It doesn't flow, there isn't a whole lot of detail... lots of Gundam-esque plots and references (I'd suggest always stating where you got an idea/mecha/skill/character from, at least when it is that obvious, just so no one accuses you of plagerizing).
There are Power Issues, with your Mecha, and your character. If it was up to me, and I was running a Mainstream Gaia type roleplay, I'd probably tell you to hit the drawing board. (Also part of why I wished you would have pointed out any parts that have been roleplayed or not. At least to me, a character with roleplaying experience gets to "Get Away" with having more power than a fresh character. Because they've grown, they've come up from being a rookie to being God the hard way, not just because you tossed in a few paragraphs in the course of 10 minutes to say they gained these powers. But because you spent months, years even, gaining them)
For one... the Character has no noticible weaknesses. Think of it in terms of a WoD character, for example. And that you start off with some points, say, 3. 3 points can be three things you have going for you/are good at. For example, being Rich might be one. Expert Marksman might be another. High Tech, top secret gear could be the third. And that's fine. Three things going for you, with your personal wealth not really effecting Combat situations, is fine. No real need for weaknesses.
But as is you have a Mecha, capable of Flight and Ground Operations. With enough power to blow up the GN by itself. (Note: If you have something that could defeat armies by itself, it's probably a sign you're overpowered) With, as you said before, Long, Medium, and Short range capabilities, with a high defense and durability... (I can almost let people slide on Overloading with weapons, if they adopt the Glass Jaw, one good shot I'm down, type)
As well you're personal character is a scientific genius. Has telepathic powers. Is a mechanical wizard and expert pilot, oh, and also has nanomachines and other implants that put him at Beyond Normal.
If you count it up like I do, that's... about 11 "Strong Points", with only one noticible weakness (This Zeon/Born Destiny force hunting him... which doesn't seem to be much of a drawback as your history paints you as being much stronger than them, capable of fighting off regiments, even when they have backup from one of you 'equals')...
Also... those Code Names make me sad.
wink But then most codenames are laughable.
So I'd suggest toning down the abilities of your Mecha, and your character, at least a little. And throw in some flaws. Flaws that matter.
Like the Sign says...

Think of real disadvantages your character (Like most people) has to face. The Hunted by the BD is a good start.
If you want to keep your character as is though... I'd probably say... add in 4 more Real disadvantages at least.
For example, you could copy the Space Elf (Or the Trilogy "Axis of Time") and have in "Lack of Resources". Now in the GNG they don't have the budget/parts/materials to repair your Gundam. So that as you use it, and take damage, you can't repair/replace what you're missing. And eventually, you'll basically be retrofitted to whatever is standard for the ASDF or whatever branch you join.
Another you could possibly come with, that follows the "Lack of Resources" is that whatever Fuel you use is hard to come by. Think... The New Generation from Robotech. Their mecha used Protoculture. Well, there were no more ASC bases, or REF/RDF bases, so every bit of fuel they had (And missiles and ammunition supposedly), they had to steal from the enemy Invid.
So saying something like the only adequate supplies you can get would be from the BD forces chasing you (Thus requiring you to go into combat and risk life and mecha), and salvaging from their burned, blasted husks.
But for the most part, it'd be easier to just cut down a little bit on your Powers. Make the BD a bigger threat to you, personally. (I wouldnt' suggest having them do full assaults on the ASDF, or wherever you're stationed, without Mod approval. But things like Spies and Assassins after Gold alone would be acceptable I bet... and ones that pose an actual threat to him) Or maybe have the BD randomly ambush you while on patrol.
Also I'd suggest you keep your Mecha Modding hands to yourself.
wink You know, do the Max Sterling thing. (Again, Robotech, Macross Saga this time), where he customized his mecha to be more responsive to his needs, his patterns, his control style. So it was Enhanced when he piloted it, but probably would do worse if someone else was at the controls.
Minor tweak's mostly. Don't try upgrades like "Now it can move at the speed of thought" or "Perfect Aim". Something like squeezing another 20 MPH out of the engines, or room for additional ammunition, cool.