Well, i think u are on a good train of thought. I would keep plugging away at it. I tried a d20 battletech/mechwarrior using the mechwarrior dark age minis. Since i already owned most of the battletech books, i just used the stuff out of the compendium and redid the power scale a little to better fit d20. Instead of 2d6, we used a d20 to resolve the attack. I think d20 future should work fine. d20 Mecha is a great book and i would recommend it to anyone interested in mechs for the d20 system. As for prestige classes, the mecha crusade prestige classes are good. d20 BESM has a mecha pilot class. I am sure there are dozen of other potential classes.
On a final note, when u mentioned the neural helmet, i had a thought. What if u switched some of the stats as they would translate to the mech. The mech's dexterity would not be dependent on the character's physical dependence rather their mental wit. So, why not use the character's Wisdom instead of the character's dexterity to modify the mech's actions in speed or agility contests. U could take it further and say that intelligence modifies the mech's strength rolls and charisma modifies the mechs constitution rolls, but i dont know. The question u have to answer for that further extrapolation is can a machine's limits be pushed beyond by the pilot's will. For a more cinematic game, i would say yes. For a grittier game, i would say no. However, when a machine is pushed beyond it's limits it usually just breaks faster.
Anyway, those are my thoughts. The jumpships and aerospace fighters should use whatever d20 system of air and space combat u and your group like.