I'm sure someone's mentioned a few things I'll put here, but with 12 pages for the thread I've got a short attention span. :-P
Character changes:
Add casual cloths for all the character classes. I'm sure the androids don't wear their armor all the time, so have a few different outfits for them.
More customization options:
Heads: More head types, I'd like to see a wider range of facial types and features. More head selections for androids.
Hair: More hair styles, with a selected few that are common amongst the human/newman classes.
Skin: A few more choices of skin colors possibly a few tan lines since I'm sure newmans don't wear their uniforms when we're not playing PSO

Skin layers: The addition of skin zones for each human/newman class to add tattoos, scars, and bandages.
Uniform colors: An option to change the color of uniforms. Have main parts of the uniform colors change with their own color sliders.
Accessories: Little goodies like hats, glasses, earrings, bandages, watches, things to wear around your neck...
NPC outfits to select from: I'm sure everyone wants their FOnewearl to run around in a uniform similar to Elly's uniform.
More interactive game rooms:
Shops:
- Weapons Shop: An actual shop you can walk INTO. Weapon displays to look at, a gun range, sparring dummy... ect.
- Items Shop: Another shop you can walk into, look at what the products look like, buy accessories, and the forbidden sweets.
- Armor shop: Another shop you can browse though looking at armors, shields, slot items, and a dressing room where you can try on the armor, shields, and slot items.
- Android Accessory shop: I don't trust the medical room to hand out $10 trap refreshments ^^, a shop just for androids where you can try out various body types for your class, head types, customize colors... ect.
Service Areas:
- Transporter: Instead of boom there's the trasnporter, have an actual departure area with seats, the ability to take a shuttle to Ragol, people to talk to, and a transporter control team you have to talk to before transporting/taking a shuttle.
- Guild Counter: Another place you can actually do stuff in, one area for Ragol missions, private missions, and ship based missions.
- Principal's area: Have actual activity instead of the people there just standing around.
- Lab area: More areas to explore, lab technicians to speak to, secret missions to find...
- Medical Room: Again a more interactive area, have a waiting room with main counter, a few treatment rooms, more people to talk to, secret missions, and have on the fly rendered scenes where you can see some treatment being done on your character (not everything though) and a random amount of time before you're regenerated after that vicious rappy attack when you weren't expecting it.
Missions: Have some missions that require the player/group to go to an area of the ship for more information/preparation/meet NPCs... ect. Such as reporting to the lab for equipment, reporting to the Medical Room for preventive treatment when going to new/dangerous areas, get mission oriented equipment...
- More missions for offline mode, Oh look, even though I've gone through this with Shino 3 times before she still doesn't get the idea to save her butt...
Areas:
- Forest: First area nice and sunny warm with an average temperature of 72 degrees... A little weather variety!! Rain, varying temperatures (affects your character's response time, too cold you have to stop to warm up, too hot your character passes out for a few seconds) snow, mud, ice, loose sand, gravel...
Caves: You'll need a device to protect you from the immense heat of the lava (if you don't you'll pass out - you get the device after awakening in the medical room after your first visit to the caves) Poison doesn't just eat health, but slows your character response times, you can't run, you stumble and fall until you use anti, an antidode, or an injection from the Medical Room to cure you from poison, and one to protect you against poison for your visit in the caves.
Mines: Add a few danger areas, where you must avoid live wires, haywire machinery, arcing energy, fire, and oil soaked areas. When enemies shock non android players they throw back the player a short distance and additional damage is taken. Player reaction time is slowed for a short time. Androids need to reboot their systems... Non android players when injured by danger areas may suffer wounds that require treatment from the Medical Room, some areas require some device/shield from the lab to safely get past...
Ruins: First visit to the ruins you get sick from the vapors from the wall puffers and need treatment in the Medical Room, you can get injured in danger areas where things fall from overhead, damaged parts, ect...
Episode II:
Beach area - Your character can opt to wear the proper beach attire when in this area, you can get poisoned, hurt by some plants and small animals (non enemy) requiring you to seek treatment. Danger areas such as sharp rocks, dangerous plants, falling objects, cave ins ect... Characters wearing heavy clothing would have a high chance of fainting, androids would overheat without special devices... Human/newman characters would have an ability increase while wearing beach attire. Sand would slow down androids.
Jungle area - much like the beach area. Areas could cause your character to get tangled in vines, heavy underbrush, slip, fall, and get bogged down in wet areas. Heat would also play a role in hindering your progress.
Mountain area - Much colder area of Ragol, human/newman characters would need heavier clothing to withstand the colder temperatures, androids would have an ability increase due to cooler operating temperatures.
The tower: Keep the same but add NPCs who walk around in the safe areas. They may or may not attack you...
Underwater research facility: Add areas completely underwater where you would have to swim to get to some areas. Enemies in the water can attack you forcing an underwater battle. A button would be assigned so your human/newman character could get a breath of air before continuing. Androids would have to seek ramps/ladders to get out of the water (you can't swim, only sink). Again some areas/creatures would cause a status ailment requiring treatment from the Medical Room.
A deeper and more sinister experiment has been done in secret on Ragol's moon...
Just a few ideas I had when playing V1 on the Dreamcast that I've kept to myself. ^^