CHARACTER STATS

You need to have a baseline in mind. Just adding stats randomly all over the place will result in disaster.

Learn the damage forumlae you will be using (in 2k3 you can find these in the help sections, in VX/A you can edit them yourself in the skills tab) and then from that you can work it all out.

I always start with health, personally. I say to myself "Right, the Knight class will have 1,000 hp". I know that the damage formula is atk*4-def*2, and I want him to be taking around 150~200 damage per turn. So this gives me the next stats: enemies should have something like 80 attack, and my Knight should have around 85 defence.
Magic attack works out similarly to that, and AGI can be pretty much whatever you want it to be, since the only stat it's (typically) compared to is other characters' AGI.

It's just a process thing; once you get the first stat set in your mind, you can start to build the other stats around that. Although don't be afraid to go back and change them if it's needed.

How fast they grow is important too, obviously, not just their starting stats. If the player's power grows too much, then killing things from the previous dungeon for gold and exp becomes faster and more effective than moving on to the next one. If it grows too little, he can skip battles and possibly even entire dungeons without suffering any meaningful penalty. Let's say, for the sake of our example, that you want the the player's survivability to be two-thirds as high if he skips all the battles in this dungeon and goes straight to the next one. In other words, either he takes 50% more damage, or he takes the same damage but his HP is only two thirds as high. How much his offense grows needs to be decided also, but let's just look at defense.

First you need to know how many levels the player is expected to gain from this dungeon. This can be a dilemma in itself - you want the xp curve to be steep enough discourage the player from going back and fighting weak enemies, and also steep enough to discourage the player from becoming twice as high a level as he's supposed to be, but you want it to be flat enough that he can gain multiple levels per dungeon and still feel like the enemies are somewhat worth fighting by the end.

Once you know how many levels the player grows, and how much their survivability should decrease by skipping the dungeon, you have different ways of giving them that survivability as they do the dungeon. If the player gains defense, their healing spells will become more useful - if the player gains HP, their healing spells will become less useful unless their willpower (or whatever stat affects healing) grows by the same degree. If the defensive stats come from stats you gain at level ups, the monsters within the dungeon will be vastly harder at the beginning than at the end. If the stats come partially from equipment you find in treasure chests, that power will come in periodic surges. If the defensive stats come mostly from equipment you can buy in the next town, the dungeon will stay at a much more similar difficulty as you fight through it (you're gaining a few stats as you gain levels, but you've also run out of MP and items by the end). If the shop sells the equipment for gold, the player is hardly penalized at all for running from all the battles or skipping your option dungeons. If the shop synthesizes the equipment out of items dropped by the monsters, the player is strongly coerced to complete the content before moving on.