Well, it sounds like you guys have already planned out how you're going to set things up, and I'm sure they'll be good, but still, I would like to give the go ahead about how I think things would have worked out.
The Guyver isn't a weapon, but as humans were created to be, it capitalizes on those attributes and makes them into warriors. But as it's not an actual weapon, it can only enhance a human so much.
The Warrior Guyver, as was stated before, is supposed to be a Guyver's peak. An actual weapon designed to enhance the weapon known as man. So of course the Warrior Guyver is going to be stronger than a standard, as that was it's purpose.
The Gigantic though, should have more power, overall, than the Warrior Guyver, and my reasoning is this. While the Warrior Guyver is a Guyver at its peak, a super-human brought to their max, the Gigantic would be like taking a human and turning them into an Ogre. Such a beast is of course going to be stronger than a normal man and be able to tear him apart, but with his larger size, is slower than the other. Someone stated that before.
For the Gigantics on the Warrior units, I don't think the power increase should be as significant as it is from Guyver to Gigantic. The large increase in ability from Guyver to Gigantic is that need for power, the need to be stronger so they can fight their stronger enemies. As the Warrior units are already powerful, they of course wouldn't have such a dire need for strength, and upon obtaining their Gigantics would receive a gracious, but not totally exceptional increase.
To explain it differently, I'll use some figures others have thrown up.
If a standard Guyver is labeled as 1x power, and a Gigantic is placed at a 5x, make the Warrior at a 4x level. For a Warrior Gigantic, rather than increasing the power by 5, make a smaller jump, such as bringing it up to a mere 8-10x power. So while Guyver to Gigantic would get a 5x bonus(At least strength-wise), the Warriors would only receive a 2-2.5x boost.
Looking at Matrix Warrior Guyver and his Dreadnought form, you can of course say he is only receiving a 2.5x boost in strength, but when comparing MWG to a standard Guyver, that's a rather incredible boost.
As for him, I believe after bonding with the Matrix, he should of course receive a boost in power, but it shouldn't be so dramatic. Instead of a 250% increase in strength, he should only receive a 25-50% increase, which would still be quite noticeable.
By working this this way, everyone can still receive their powers and boosts from the changes in the stories, but they won't become god-awfully powerful.
Following it this way, since the later Guyvers tend to be placed so they can keep up with Dreadnought, as he'd of course be weaker by using this method, they would be down-toned as well. All these insane figures would be brought down to more manageable levels that could help put things at ease. For, not only would the various Guyvers be lessened, but so would the higher Chronos units and the like. I mean, it eventually reaches the point were low level Zoanoids and standard Guyvers need to just go into hiding so they aren't killed. If smaller boosts in power were put into effect, they wouldn't be so easily discarded and could still make a difference, even if it's only as distractions or with mass numbers.
So, those my thoughts on all of this.