Yeah, I noticed that a lot. I think the main saving grace that prevented that from annoying me too much is that, if you know what you're doing, you can at least fight great grind locations shortly before the two bosses where a little extra work might be needed*.
* That is, if you're trying to explore dungeons thoroughly and all; if not, you might be grinding to beat the final boss in C1 and C2, also.
1. In Bloody Mary's castle, there's a side room with a durable suit of armor. Run in, kill, run out; repeat as necessary.
2. All through Beruga's Lab and Airship, there are big robots worth a lot. In the big room with all the little rooms where you and three allies press switches to get to the airship, you can go into one of those side rooms (the one with Perel), go out and take out one of those robots without much risk.
So at least the game was considerate to give you easy grinding spots. Although it does completely crack me up to cause 15 damage a hit, gain one level and two strength points and then be doing 50 damage. At times, that's pretty cool, though. I know entering Chapter 2, the Ra Tree starts out feeling like this brutal dungeon. It's larger and less linear in appearance than the C1 towers and the regular monsters are tougher (and you don't have the "gain HP from early-game weapon" benefit you get down in Crysta with the Crystal Spear, so health items are more necessary, as the only place you need them in C1 is the boss of the final tower). And then I'd gain a level or two and just cruise through everything. It is nice to see real, definite power gains after going up a level or two.
I'm not afraid to die because I am invincible
Viva la muerte, that's my goddamn principle