The cool thing is right at the beginning of the game it tells you that you can find save points using the minimap.
yes I know... but if shows only those you have already found.
The minimap *does* guide you to save points - you know how it shows area exits as white circles? It shows save points as red circles. Note, that's the *mini* map, in the corner of the screen, not the fullscreen map. Those circles give you the general direction of a save point (the game teaches this by talking about how your home is displayed by yellow circles). And the save before the boss is pretty darn close to him. Me, if I reach a boss (and lose) and see there are still areas I haven't explored yet in that dungeon (that aren't blocked by something I can't get past), I go back and do some more exploring. This not only lets you find important things like save points, but you can also stock up on more cooking ingredients, maybe find a recipe or collectible that you may have missed if you beat the boss (as most people will leave a dungeon the moment they've beaten the boss and gotten a new ability).
As for the mithlas boss, I didn't try to kill it by just shooting it, because the first couple major bosses wasn't killed that way (one by singing, the other by luring it into a zapper thing). Took me a bit of time to figure that out on the second boss, but once I did I figured out that all the major bosses were puzzles, and not to be just shot to death. Of course, then the sun boss threw me for a loop

In the end I just gathered all my healing/defensive items and tried to wear the boss down...and it worked. Yeah, there are a couple tricky spike jumps before it, but only a couple, and if you know you are going to be hurt, just farm up a couple more healing items.
I actually like this game for a couple of the reasons the OP doesn't - the game doesn't give you hints on top of hints on top of hints - it actually lets you think, explore, and experiment and try and figure things out for yourself. Aquaria gives you just enough info to survive in the world, and the rare hint here and there about something that wouldn't be obvious to the player (like the gears in the sun temple), and then lets you go and explore this new world. It's not just mindless "go from point A to point B, attack boss until dead, repeat" This is a reason I've been disliking a few of the recent Metroid games, they continually give you hints, tell you where to go next (marking it on your map), and what to do. You scan a boss and it tells you his weak point. Even Zelda has been getting simpler lately, as, while they don't tell you boss weak points, they make sure the weakness is *ALWAYS* the item you just got in the current dungeon.