I actually started a file where everyone got to lvl 99, but I wanted to get all of their stats (through magic tabs and whatnot) maxed out as well.... I did EoT runs, where I would plow through the game, beat Red Nu, get the +10+10+10, then restart. I didn't QUITE finish up.
Oh and IMO the fastest way to lvl everyone to 99 (starstar?) is just give all of your characters beserk or a frenzy band (80% counter attack rate) and put them in the beginning of Mother Brain's factory, let the thing run through, leave, come back in 5 minutes, rinse, lather, repeat.
And the 123 reset I'm sure will be repeated in future installements of the Chrono Series, I'd actually be severly disappointed if they didn't.