You can start by assigning your troops to Mobile Suits and Armor from the various Gundam series, or you can develop new Mobile Weapons to be added to the supplies menu. The machine you develop will be priced appropriately, and no matter how advanced it is it WILL need repairs. It's best to develop cheap Mobile Dolls to use as initial troops, create one or two Mobile Armors for large assaults, and make advanced Mobile Suits for your most elite pilots. Then there's the matter of your personal steed...
You can customize your character's appearance to a minor extent, as well as select from several voices or record/download your own (this would take a while, as you'd need to record various grunts and such). While most of the battle will find you giving orders from your ship (or not, your choice), you can board your own customized Mobile Weapon whenever the need (or urge) arises. You won't have to worry as much about costs aside from the initial upgrades as, if your machine is destroyed, you are as well. You can choose to pilot a Mobile Suit, Mobile Armor, or one of those little one man Star Wars type fighters. You'll also be able to customize your launch sequence and even theme song.
You'll be able to recruit various preset pilots for your fleet, but you can decide what their training programs will be like. Your pilots have specific natures that determine what aspect of combat they would be best in, and training them in opposing aspects may convince them to leave your team. However, you can train most pilots for most jobs. Certain pilots may also be unique in ways that can only be observed on the battlefield. For example, one of your pilots may be adept at dodging enemy fire. These people are often candidates to be "ellites", pilots who will lead the charge against enemies and directly assist you when you join the fray.
As the commander of a fleet, you'll need a ship from which you'll coordinate your attacks. Aside from color scheme and decal, you can add beam cannons, hyperlasers, and various other weapons to your ship. If your flaghip is shot down, whether you are on board or not, you'll lose, so make sure it's well fortified.
Obviously, you can't just pack on more and more heat and send a single juggernaut out to destroy your enemies. Ammo isn't infinite, and replenishing heavy weapons can get expensive. Also, even if your upgrades fit, they can seriously hinder your machine's movement. Putting too much power into it can also cause the core to overheat, or at least be more prone to rupture from an enemy attack.