I've been looking for people to talk 3ds with! I picked my copy up during the crazy Black Friday sales--since you are still getting the 3 starter pack figures with the game, the absolute lowest price you'll find (short of used copies) was half price, which is when I got mine.
As for your question about 'storing' 3 characters--what they actually mean by this is that you can have up to 3 active characters on your console at any given time, excluding the 3ds-exclusive 'gold' characters that can be unlocked via performing certain tasks within the game (i.e. no figures exist for these golden guys. The lineup is identical to the crystal series of figures.) As you level up your characters, you can swap in other characters for your team, but their data is all stored on your cartridge rather than on your figure, unlike in the regular console game. The only thing that the 3DS scanner writes to the figure is the fact that it's been used on the 3DS, and will give you an extra spin (one time only per character!) on the main game.
So, let's say I have Rapunzel, Jack, and Sully stored in my cartridge at levels 4, 6, and 8. Let's also say I just got the Cars playset and feel like swapping in Lightning and Holley for some new stars. I can then scan in Lightning & Holley to replace Rapunzel and Jack, and then level them both up to 4. I can then scan Rapunzel and Jack again later, and they will still be levels 4 & 6 where I left them.
In summary here, the character scanning 'activates' the character on the 3DS rather than actively read/writing to it like the console version does. When you think about it, this method is in fact more practical given how you're only relying on 3 AAA's to power the scanner.
And for those of you who are curious, all skydome/terrain power discs unlock custom dice, which do NOT in fact do anything special other than "oo that looks nifty". Toys are the most useful discs here, and usually turn out to give you more boosts than anything you can unlock with characters, even though unlocking stuff with the characters takes much longer. Additionally, the MagicBand unlocks the Disney dragon, which in this game replaces the Star Command drop ship to plunk your bonus emblems onto the game board. (Yes, it actually does something here too!)
Edit: If you're actually wondering how much I've done with this game, I've been extremely bored so I've managed to nab 99 stars as of yet. The working pattern for your store unlocks is apparently 1 toy + 1 building + 1 decoration for each tier of stars you hit. I've gotten all the boards cleared and hidden stars + adventure goals and scenario mastery stars. Just need Infinite Mickey for the last one!
25 stars =
Identity Disc (Tron) + Combat Simulator (Toy Story in Space) + Basic Alien (Toy Story)
50 stars =
Scrooge McDuck + TRON - Billboard + Topiary Mickey
75 stars =
Slapping Prank (It's actually the Sticky Hand from opening up Mrs. Incredible's character chest in DI) + Scrooge's Money Bin + LuxoLamp
90 stars =
Recognizer + Christmas Tree + Incredibles Statue
100 stars =
Crystal characters are also different in that they are completely separate characters from their normal counterparts, with different items/stars/powers/stats to unlock. Until they reach level 9, however, their stats are really kinda junky, and only half that of a normal character at the same level. Once they hit 9, though, their 2 main stats are completely maxed out, which makes them great additions to a team because they can cover 2 of the 4 stat categories for the adventures. (Oh yeah, they also have 2 main stats instead of only 1 that normal characters do, and Mickey gets ALL FOUR stats maxed out!)
Another thing I've noticed is that there is actually one more character slot than there are actually characters in the game. Does this mean there's another secret release figure that nobody knows about yet??? (maybe it's that glowing Buzz!) Getting every character to level 10 didn't unlock it.
Characters leveled to 10 so far:
Woody
Buzz Lightyear
Jessie
Mr. Incredible
Mrs. Incredible
Violet
Dash
Syndrome
Lightning McQueen
Mater
Holley
Francesco
Sulley
Mike
Randy
Jack Sparrow
Barbossa
Davy Jones
Wreck-It Ralph
Vanellope
Jack Skellington
Anna
Elsa
Rapunzel
Sorcerer's Apprentice Mickey
Phineas
Agent P
Infinite Buzz Lightyear
Infinite Mr. Incredible
Infinite Lightning McQueen
Infinite Lone Ranger
Infinite Sulley
Infinite Jack Sparrow
Infinite Agent P
Infinite Sorcerer's Apprentice Mickey