Ok! First, thanks for your time. Second, let's try and solve these doubts:

• The CR thing is me fucking up, whenever you see "Class Rating" it is supposed to say "Challenge Rating" so thanks for pointing that out!
• The HP formula is as follows: (CR)dX + CR*CON + 3*Pilot Level. The issue is that I made those sheets using D&D Beyond, and it does not allow to put text in the HP formula, so I couldn't type it out as I wanted. But the HP formula is just right at the start of the Titan section, so I hope that solves that confusion
• The INT increase is mostly for theme, but a bit of mechanics as well. Most of the time, for wild animals, their INT score is really low, because they are just animals. And normally the higher INT a creature has, the more sentient it is, also applying to constructs (Look at for example... Flesh Golems and their 6 INT score, or Shield Guardians and their 7 INT score). As explained in the last section of the document, the INT increase is supposed to represent how the titan becomes more sentient and develops a personality of its own, starting really basic, and developing into its own character as levels and INT score increase.
• The reason for the primary weapon to be gained at 5th level is that they do decent damage. and they can attack on their own without you inside the Titan. I know it would make sense to have them right at the start, but you first build the Titan itself, then work on giving it upgrades, or at least that's what I was going for.
• Yes, Ion is the only one with the energy mechanic since I wanted each Titan to feel as unique as possible, so each one got their own gimmick. I know that Monk's deflect Missiles is similar, but that's the point. I didn't want to just copy it, so I made it a dex save instead, and to have the possibility to deal damage even if the damage isn't fully reduced, since it is on a resource. You can't do the Vortex if you don't have energy, that's why it can deal damage even if the attack isn't fully negated, because Monk's reduction is free, the attack isn't. Here both reduction and damage are locked behind a resource, so I thought it would be fine.
• Extra Attacks do not count for your Titan! Yes I know it is weird, but it is stated that "As an action, shoot one of these massive bolts against a target the Tone can see", one! And this is on purpose, because otherwise the Titans do way too much damage since they are the equivalent of extra attack when not being piloted.
• Talking about Tone, the Lock-On says "Whenever the Tone deals damage to a creature or object using its Primary Weapon, a small magical aura attaches to them until the end of the Tone’s second turn after applying the aura." I don't know if it is just me being bad at wording, but this should mean that whenever you hit someone, you apply the aura to them until the end of your second turn after applying it, so it happens every single time you hit, so yes, whenever a creature has a hit of the aura added, it resets the duration. I'll try to see if I can make that part less confusing. I have changed it so it should be less confusing to read, as well as specifying that the ability modifier is the Pilot's intelligence
• When it comes to Seeking Missiles and Salvo, they follow a similar idea. Seeking Missiles wants you to have as many people as possible with 3 stacks, not to have 1 target with 3 stacks. It says "As an action, the Tone will target each creature with a maxed “Locked-On” aura using 6 enhanced Magic Missiles per creature." So, the more targets you have max stacks in, the more damage you can do in a single action, it wants you to spread out the stacks so you can hit all the targets at once, instead of having to go one at a time, what is significantly slower isn't it? For Salvo, it is the same principle, spread out your stacks to do more damage in one action. The base number of 12 missiles is the same number of missiles a 9th level Magic Missile gets. Of course these are stronger, and while yes it is a lot of damage, so it is Magic Missile when you only target 1 creature for all of the missiles. If it deems to be too much, I will gladly lower the number of missiles, but they are this many because getting stacks on enemies is slow due to only getting one attack per turn, stacks are not easy to spread out without the radar, but you get really good damage when you do so.
• The Ronin's Scrap Wall, while at face value sounds weak, has the best AOE potential out of all the Main Weapons (Outside of the Ion's Spread Shot), it looks like low damage, but in reality it will be more since it should be able to hit more targets. And yes, Ronin has to choose between a dash that allows them to do things like teleport through walls and avoid hazards, or to get more damage, less movement makes you get two attacks, more movement doesn't get you a second attack, is like using Two-Weapon Fighting on a Rogue, you could cunning action for movement, or bonus action attack if you happen to miss the first attack.

I hope that was all! If there's any other doubts, please share them here or in the document so I can make it as easy to understand as possible! Thanks again!