For starters, the "world shells" in Septerra Core seem very similar to the "lagoons" in Bahamut Lagoon, which are basically floating land masses (also like the Magical Kingdom of Zeal in Chrono Trigger, but not to the same extent). Though I've seen quite a few fantasy games with floating islands or castles, non of them had the whole world like that as in Bahamut Lagoon and later, Septerra Core.
As for the Chrono trigger references, aside from the unique speed/turn based battle system that exists in both games (with a minor difference in Septerra Core, there's three levels to which a character's speed/turn bar can charge instead of one), a lot of the characters in Septerra Core seem to be based on those of Chrono Trigger. I'll list these below:
Maya for example seems to be based on Marle. They just changed her hair to blue and gave her a rifle instead of a crossbow (both of which are similar). Going from a princess to a "junker" was quite a bit of a change though, heh!
Grubb and Led are based on Lucca (all three being mechanics that work on making and repairing robots).
Corgan and Araym both also seem to be based on Crono in different ways. Corgan is a swordsman and is a polite person who is always looking to help others for a just cause like Crono. Araym on the other hand has pretty much the exact same hair style and color.
Runner and Lobo seem to be loosely based on Robo. Runner uses the same type of laser based weapons and bombs, whereas Lobo is a humanoid robot (or in this case, a cyborg) like him with a very similar name. It seems to me as though they broke off Robo into two different characters, one that looks like him and the other that uses the same type of weapons.
The Mining Helgak (an enemy boss on Shell 7), looks very similar to Lavos and his spawn.
Selena doesn't seem to be based on any character I know from either of these two games, though she and the symbol on her cloak does remind of the main character from Chaos Legion.
And last but not least, Badu also looks like they loosely based him off of Frog. Though there is enough differences between these two characters to call them unique. If anything, he looks more like a primitive Protoss (Zealot) from Starcraft, hahaha!
Well, that's about it. So, what do you all think of this? Is this all a coincidence, or did the Septerra Core staff copy a lot of elements from these two classic SNES RPGs? And before anyone gets upset, I just wanted to say that while I enjoyed playing Septerra Core for the most part, a lot of plot elements and even characters seem to be copied off of Bahamut Lagoon and Chrono Trigger. It's not like I hate the game or anything, I'm just saying...
Edit: And one last quick note, the world of Septerra also reminds me a bit of the artificial satelites from the Panatasy Star series, namely Phantasy Star 3.
Edit 2: The core energy thing is also pretty similar to the whole "mana" idea in other games.