Good points all around.
As I said, this was an experiment and your criticism is well appreciated.
Let me address your points in order for public self reflection:
You went way overboard with the mage's squishiness. Unless he spends half his stamina on his barrier, doing anything else than defending is risky. As it is, I never used his offensive spells. Instead I used him as a stamina dispenser. When only one enemy was left alive, I had him cast regain stamina on whoever needed stamina and had everyone else defend. Once stamina was fully restored I killed the last enemy.
I suppose his stamina amounts, as well as his squishiness kind of did him in. I would like to stress, though, that my testers found constant use for his attacks spells without using barrier. His low HP did not pass over my head, nor did his defense, but I did test him and his attacks out in battle - he does splendidly well.
Fixes that will be made in future projects: Slightly healthier mage who can survive the first round of battle without high cost supplements.
For boss battles I had him cast regain stamina until he inevitable died. Then I just left him dead.
I addressed that in the previous point.
The characters have way to little stamina. Unless you abuse regain stamina, you will run out really fast and the regain stamina method is annoying. Limiting their stamina so much just makes the game more annoying, not harder.
This is part of en experimental whole - I despise using the large numbers RMVX provides for random graphs and thus I divide all random graphs, still on the basis of A-E, by 10 to arrive at saner and more comfortable numbers. While I don't think that breaking stamina out of this pattern would work, perhaps modifying the costs to have them last longer. I admit some things were a bit over priced. Part of the experiment.
Fixes that will be made in future projects: Lower relative stamina costs and more, less annoying, ways to regain stamina. Additionally, experimentation with slightly larger numbers.
The blessed water vial is overpowered. You can use it to make the mage less squishy, but you can also use it to make the warrior invulnerable. With it equipped as well as the best armor available, no enemy can deal more than 1 point of damage (except maybe for the big scorpion). Try it against the orcs, even if they kill the rest of the party it doesn't matter since the warrior can easily solo them.
There is one thing you have to understand about defense, the more you already have, the more effective additional points are. I think one point of defense reduces 2 points of damage in RPG Maker VX. Let's now say an enemy deals 10 points of damage. One extra point of defense reduces damage from 10 to 8. That's a 20% reduction. A second extra point of defense reduces damage from 8 to 6 which is a 25% reduction. A third makes it 6 to 4 which is a 33% reduction and a fourth makes it 4 to 2, a 50% reduction. Finally, the fifth point reduces damage to zero which the game seems to handle as half the time no damage and half the time 1 point of damage. 2 points of damage to an average of 0.5 is a 75% reduction.
Point taken about the defense values, as well as the overpoweredness of the vial. I never was able to quite follow the damage formula and balancing of battle in that regard, and neither does the help really provide a comfortable reference and explanation. However, this short comparison you provided does help.
Fixes that will be made in future projects: Better thought out defense scores. Larger numbers might provide an easier fix.
For that reason you must either make sure no character can come even close to almost negating damage completely or you need different damage sources, like magic. Let's say that enemies sometimes uses magical attacks. Even if the warrior is invulnerable to physical attacks, once his allies dies he's the sole target and an unlucky round with a lot of magical attacks could do him in. In this case it will be more attractive to give the other characters more defense so that they don't die and the warrior don't have to be the sole target. As it is, it doesn't matter if the warrior ends up being the only one alive since with the BWV he's practically invulnerable.
I really should have thought about the warrior as a spell target. Was thinking low level and found out you don't meet a lot of low level spell casters as monsters.
Fixes that will be made in future projects: Balanced chance of survival for the whole group by adding more diversity in damage from enemies. Continued from above - fine tuning defenses.
I suggest you try varying things a bit. Add magical attacks and maybe also defense ignoring physical attacks. See if you can find other ways to make enemies differ from each other besides giving them different stats.
This being about the monsters, though I can also apply it to characters to an extent, I will take to making better.
Fixes that will be made in future projects: Variant monsters with inherent differences.
Thanks for the criticism, which will be used in favor of creating better experiments to fine tune my game creation style.
On a side note, could you PM me some examples of monster variations? Not entirely sure how I would go about it.