Okay, observation: there's a line in the Main Weapon upgrade that specifies what happens if an in-built weapon is Heavy. You can't get
a heavy in-built weapon (save for Real Robot multiclassing, which just seems weirder: Real Robots get a bonus effect out of a Super upgrade?)
Regeneration seems hellishly overkill. Get it fully upgraded with a Super Robot that's poured all its points into health and regeneration? 160 (+1.75) HP back. Per turn. Get two things like that, without any save or die effects, and they'll be firing away forever...
And now... a short version (because it's too late at night for the long version) of something that's been bugging me all day: Real Robots just seem plain better
to go for than the Supers. They get power jumps, yeah, but the tiers are fully competitive right before upgrading, and they get better Arsenal stuff at the same time as better robots. The gap just never seems to close.
Hell, take their class abilities: average difference of 1 hp isn't going to make a big difference, both have full BAB and one good save, Real Pilot has more skillpoints, same proficiencies. Okay. Next? Well, the Real Pilot gets more bonus feats, but less spirit and doesn't have the favoured maneuver ability. Fair? Doesn't really seem like it: one bonus feat all but erodes the difference in spirit, leaving another two to do whatever with over the super pilot. Maybe the +4 to Pilot Level of one maneuver (and +3 to another, etc.) might make up the gap? Not really expecting so with the large save bonuses everywhere, honestly. And finally, capstone: the super pilot gets 4 upgrade points that cannot exceed HD caps, the real pilot gets another Arsenal weapon.
See, there's a bit of a problem: if a Super Pilot puts 63 points into the straight numerical bonuses, that leaves them another 17 points to play with. Now, what upgrades can be achieved with 4 points? Growth? Well, if you haven't spent it before, that's straight from Medium to Colossal. Higher damage (do the Arsenal weapons even scale?) but suddenly all those targeter upgrades and AC boosts are pretty necessary. Transform? Well, the one option might be handy. Basically, you get a small bonus (because they can be picked at any level) to any one thing. Now, if I'm a Real Pilot? I can grab any of the special weapons if they'd be handy. Any basic weapon that would be useful but isn't already squeezed into the mecha. +6 to dodge and reflex saves (firmly beating whatever the Super Pilot can achieve with the same thing), +8 to all my attack rolls, or--and here's one of the most ridiculous--+8 to dodge and reflex, +10 mu to speed, +10mu to range, and +4 to attack rolls.
Real Robots also have better weapons to start with (aside from anything else, the fact that they get multiple types and everything automatically has a weapon doing more than 1d6 damage or special abilities) and, in general, more access to abilities (especially weapon). The one
thing they cannot pull off is regeneration. Everything else? They're going to do just as well or better.
In short? Most of the Super Robots' upgrades are going to go towards keeping pace with the Real Robots' stats, including getting more Arsenal access, to things that are a step behind. Now, there's something strange going on when the key feature of one class is used by the other to keep up with them. :/
Thematically, it seems rather weird, anyway: Super Robots with a modular, now-use-this thing design seem to be the exception rather than the rule. The upgrades don't really offer much in the way of customisation; if you want a choice of weaponry, it's better to go raid the Arsenal than invest in your inbuilt stuff. Upgrade points come off less as a custom mecha and more just working out how the chassis is balanced before you put on distinguishing features, which can be easily interchanged.
What Super Robots look likely to really shine at is... stealth, due to miniaturisation.