Alright, I'll answer my own questions, along with some others.
1: If I was going to do the pilot, I would make it a 4 parter like Sonic Underground did. While I did not like how it was executed in that mediocre at best show, I do admit it was nice to show Sonic developing as a hero. So, for Part 1, I'd show how Sonic and his friends cope with Robotnik's invasion and trying to survive on their own, especially once Rosie ends up captured and roboticized.
Part 2 would introduce Tails' arrival at the Great Forest and how Sonic would discover his hidden abilities when fending off Swatbots when trying to apprehend them both. Then, Sally would later discover Tails had great power within him after doing some investigating about his background. Part 3 would be about the team's first mission together invading Robotropolis when around the age of 12, and Bunnie not being experienced, ends up getting captured and nearly fully roboticized, barely being saved by Sonic and Sally in time.
And for Part 4? It would about 3 years later where the Freedom Fighters have now upgraded their base and arsenal to be a real threat to Robotnik. And after they put a major dent into his operation during their latest invasion, Robotnik would retaliate by going with a massive invasion of the Great Forest, planning to burn it to the ground, only to be outsmarted yet again thanks to some cleverly hidden Krudzu plants around it by Princess Sally. Driven back once more, Robotnik at the end vows to unleash his secret weapons on them to finish them off once and for all, none other than his duo of Metal and Silver Sonic.
2: Well, anyone's who read my fics knows I would indeed do that. And like Redstranger mentioned, any added characters' backstories would be refined and reshaped to fit the Satam universe. They're not going to be added recklessly. Any non Sonic Satam character added to to the story will have a purpose or won't be included. And the reason why I would is because I believe the Satam universe should be THE MAIN universe of the Sonic canon, not the games. Nothing against good game universes like Sonic Adventure, but I believe even that story could be reshaped to fit into the Satam universe as well.
3: Yes, I would expand upon their battles. For starters, I like the idea of them winning as a team because of their strategies and perseverance. One of my biggest complaints with the show is how Sonic was pretty much did 75% of the heavy lifting. And I get it. He's the main character, but seriously, he was absurdly OP at times. I rather he be the rabbit of the team, meaning he's the main one Robotnik and his army focuses on due to his super speed and abilities, while the others set up ambushes and explosives to lure them into a well organized trap.
Same for Sally as well. Season 2 made her too Mary-Sueish at times. While I understand Sonic is the heart and Sally is the soul of the team, that doesn't mean Bunnie and Antoine, along with Rotor and the others are insignificant. Like I mentioned above, it should be a team effort, not a one man or woman show.
Heck, one of my ideas for them to beat Robotnik during a battle for territory and resources is use a strategy similar from a battle in ancient warfare where they use the wind and a double agent to set up a perfect ambush where they appear to be surrounded, and then unleash the trap, unleashing a massive EMP wave onto Robotnik's troops, frying them, and then setting fire to Robotnik's current base, using the wind's current direction to completely engulf it, forcing Robotnik to flee on foot back to Robotropolis since all of his machines are kaput.
Seriously, I would have loved to have seen more of those kind of battles because that's what war is all about: Outsmarting and out-muscling your opponent to beat them. I get the fact it's a kid's show, but there's no reason why the battles couldn't have been more than just Sonic busting up machines and Sally doing her stuff with Nicole. I get the fact that's part of it, but I want to see different strategies and scenarios to keep it interesting.
4: I would mostly keep them the same, save for a few differences. For starters, I'd want Bunnie to have more of a hatred and sorrow towards her roboticized limbs. While I wouldn't want her to be angst like Shadow, I do believe she shouldn't just be ok with this completely either. I mean, she lost half her body to the roboticizer. That's going to leave some emotional scars.
Heck, now that I think about it, all the Freedom Fighters should carry some emotional baggage about what Robontnik put them through. You know, nothing over the top, but they shouldn't be happy go lucky all the time either. Like I mentioned above, they are at war, and that's not something you just handle lightly. Plus, it'd be good character development too.
One of my ideas for Antoine to expand upon why he's a coward is because he saw firsthand what happened to his father during a mission and it nearly broke him. Even when they gave him his sword to possibly fight with, he could not muster the courage to use it because of that horrible event. His father was a big part of his life and once he was gone, Antoine lost that rock he leaned on for strength during difficult times.
Granted, I do plan on him eventually overcoming it, but not for awhile since I believe it should be in gradual steps like Archie Sonic did.
And last and certainly least, I would try to give an explanation where Dulcy came from. Like say... they rescued her from a Swatbot invasion of Dragon's Keep and they discovered, like Tails, she had great power hidden within her. Seriously, that was just so stupid how she's just there with no explanation in Season 2. I hate it when shows do that because it's incredibly lazy. Would it have killed them to have Season 2's opener have the Freedom Fighters meet her and she joins them in their quest to free Mobius?
5: As the others mentioned, I would have as well. Because hey, who doesn't want to see how our Freedom Fighters are carrying on once the war is over? So, unlike Archie's, I would have done it 10 years into the future rather than 25/30, where they're all in their late 20's and some of them even have kids. I mean, why show them when they're past their prime? That's just dumb.
As for the story, I'm still pondering it over, but for now, I'm possibly considering it be about how a treasure hunt gone wrong by Rouge and Nack where they accidentally frees Mephiles and Iblis from a forbidden chest, causing them to escape and attack Mobotropolis after it's been rebuilt, engulfing it into flames, causing the death of many civilians, including Sally's father. Blaze and Silver soon appear on the scene to drive them back temporarily, but the damage done is nevertheless catastrophic.
Eventually, they have one final showdown in the open fields where Sonic, along with Shadow join them to fight these vile creatures and finally rid Mobius the final evil of the planet.
I admit that story does need some fine tuning, but I think it could be good as a finale to the series since it'd be a great way to introduce Blaze and Silver, as well make Silver relevant by making him the strongest between him, Sonic and Shadow. I am so sick of seeing Silver treated like an incompetent idiot. I'm not saying he shouldn't have some of that to keep him balanced, but seriously, give the guy some dignity instead of always being a punching bag.