First off, I decide how what kind of scale I want to work with. Smaller numbers? Or bigger numbers? For the current project, I went with three-digit HP...and endgame attack stats of 500+, which was fun to work out a formula for. Next, deciding how much I want equipment to determine their power vs. their base stats.
Next, I decide upon the various party members' roles/classes/abilities/whatever. And based on that, I come up with rough figures for what their stats will be. I take note of everyone's Level 1 and Level 99 stats in a Notepad document and how much ticks left or right on the growth speed scale they are.
Once I have everyone having stats, I start noting their stats at various levels—15, 30, 50, etc.—to ensure that their stats have enough of a difference from early levels to late levels. Hyde having 100 HP and Attack over Radd at Level 50 when they're only 20 points apart in both at Level 20 doesn't make much sense. Tweak the values, adjust growth speed, recheck numbers, change ideas for character roles when I realize one character is just an inferior version of another character and the token "cleric" character is a stupid idea, retweak to balance out that new dynamics, and boom.
Well, there'll probably be plenty more tweaking to do, but that's the gist of my terrible, terrible methods on doing stats.