Well, I thought I'd try and add something to the Spekkio Theory, so, I'll try and refute Zeality's refutation of it...
Refution
ZeaLitY: The foreseeable problems with this theory are, a.) why Spekkio would simply not destroy Lavos himself, b.) Schala refutions (check that theory section) c.) Spekkio never explicitly claims to want Lavos dead, nor is the Entity especially affiliated with magic. Though it can create Gates, it is unknown whether magic is the mechanism by which it is done.
A.) Spekkio says that he is only as powerful as those that he faces. He couldn't fight Lavos in combat, because there is the chance that Lavos could win, if they were equally matched. After all, Lavos could battle Spekkio multiple times; Each of his outer shells forms, then his Inner body, then the core itself. Spekkio is powerful, but he may not be able to handle Lavos several times, if at each fight he is only Lavos' equal. It'd be better to give power to a group of people that have the potential to defeat him.
B.) I'm afraid that I'm not understanding this point. Could I get some clarity, please?
C.) The fact that Spekkio gives magical power to Crono and company shows support towards destroying Lavos, if he is in fact the Entity. Unfortunately, this is circle logic, but I can't think of anything for this right now. It seems to me that magic is involved in the creation of the gates, but I have to focus my thoughts on it first...