1) Suffers from combat fatigue. In some areas, thankfully, there are only one or two groups of enemies. Other areas place them every five meters. Like almost every RPG out there, hordes of low to mid level enemies take the place of plot depth (or width) and difficult battles. In this game, for instance, I would have rather seen one really difficult battle per area, than 10 battles where the outcome is a given. I've started to use the Ctrl+F3 cheat when I have to retrace my steps, which leads to comment two.
2) Respawn. Dear god, who decided to have the enemies respawn each time you leave and reenter an area? To be honest, for the most part, unless you play the game always in the wrong direction, there aren't many areas that require constant retreading. The Shell 7 mountains are, to date, the worst example, but most you go through once and that's it. Granted, that would have left conquered areas empty, but...who cares. If the battles weren't so painfully easy to begin with, players would feel pride at retreading an area they very nearly died emptying.
3) Combat: There is very little here in the way of tactics, but not necessarily because of the system. Which is what I thought initially. I think the problem here is that one has no information about enemy creatures and therefore cannot plan anything. The deepest I've had to go into tactics is against one or two of the bosses. The run of the mill battles are no brainers until one of your characters get low on health and then, rather than charging up the character, you use him at stage one to heal him/herself.
Perhaps more detrimental to combat is the lack of variety. There is no difference between ranged and melee attacks. Both sides simply pound on one another until victory or defeat. Core magic doesn't add much. It's your typical elemental inspired magic system and pretty thin, at that. I've only ever bothered to use it if I notice a boss using a specific type of attack (say fire), then I'll give water a try against him.
Each character does eventually acquire extra combat moves that require a little core energy, but, from my experience, most of them are not more powerful than the stock attacks. I could be wrong here and I'm sure each has a best applicable situation. What it boils down to, they are unnecessary.
4) Story: Story and character are two of the game's stronger points. While the former if boiled to bones is cliche, it is, because of the world it's set in, fresh. The characters are entertaining and varied. Unlike my experiences with Final Fantasy, there is a good deal of grit and darkness to the story. I would have liked to see more interaction between the characters. I would have liked for them to develop during the game. Rather, each character's story is set up in the first few scenes they enter the game and then that's it. They're just a part of the tide. Granted I'm not to the end and I can feel several characters will have big endings. Whatever happens at the end, it won't make up for hours spent hacking through levels where none of the characters turn to another and say, "I love it when a plan comes together."
5) Leveling: Rather pointless. The player has no control over it. Stats go up, is all.
6) Items: Equipment is ok. I like that equipment won't work with every character, but overall, there's little choice. You can choose to equip something that will increase your power over your speed, but I find that power boosts are handier. Since I don't use the core magic much, I don't worry about equipping core boosting items. By the time you get to where I am in the game, you have so much money, you can upgrade everyone in the next town you find. If you're studious about it, the equipment upgrades are much like leveling, in that, there's really just one choice. The only place where this isn't the case, are the special items common to all characters. However, since combat is really just a beat 'em up affair, equipping items that add to strike and power seem the best to me.
7) Main character: She's a junker and yet, the story had to include two gadget/tech characters. Why couldn't have she been the techie? She's no techie. She's not the best core user. The best fighter. The best...anything. I just quickly was let down that the story opens by saying she's a junker and then we never see it. She has to hook up with a friend who's the real junker/techie.
I realize much of the above sounds harsh, but overall, Septerra Core isn't a bad game. It's just kinda dry. I'm old enough that combat and equipment and exploration don't do it for me anymore in games. I need story and strong characters. Perhaps I should stop playing RPGs altogether and completely switch to adventure. The last RPG I bought, Arcanum, fizzled. Oh, it's a wonderful RPG, but what the RPG game industry hasn't seemed to realize, is that quests aren't story. Usually, they're just filler. If they manage to build character, it usually isn't directed toward the plot. It's just random 'goodness' or 'evilness'. And that perhaps, is the final good thing about Septerra Core. All that you have to do is somehow linked to advancing the plot.
I'll add a note here when I finish.

Re: Point 7 - A "Junker" is just someone who salvages junk. You don't need to be tech-savvy to dismantle a machine for parts. As for her role in the party, besides being the unspoken leader, she's kind of an Everyman character. I've seen this in a lot of Western RPGs that follow a Eastern RPG model; instead of making the "main" character indispensible because he/she has superior stats or plot-powers compared to everyone else, the developers make him/her useful by making him/her the most generally useful character. When you think about it, Maya can basically do anything. She's not the fastest, the strongest, the toughest, or the best at using Core spells, but she can do any task with some degree of proficiency, and outperform every other character in at least one respect.
I agree with you on the combat, though. It's intolerably slow, and in the later parts of the game it gets worse. By the endgame, I personally was just nuking every enemy party with magic just to save time, expense be damned.

Yeah, I see your point. I suppose I projected more reality than the game exhibits. I figured that one who lives by salvage would have some basic understanding of her 'product', so to speak. It's more like she's just a gal with a metal detector on a beach. If she were to find a Spanish piece of eight or a flux capacitor she would have to ask an expert what it is and what it's for. I just hope she knows what it's worth. :)

A little farther now. Just past the defeat of the three Magi.
It's getting more and more tedious. The maze-like Chosen palace levels were torturous. Pointless running here and there in order to flip switches. Ugh. And the story is getting strung out.
The only good thing is that the battles are becoming more of a challenge. I wish all the battles were like those of the 3 magi. However, the difficulty isn't derived from the intelligent AI of matched forces, but from these enemies having one killer attack that can slay with one strike.
I'll take what I can get.