Very nice analysis; Tales of Symphonia is one of my all time favorites!

Such an epic story... I agree with most of your typings.
Lloyd: Definitely ESFP. Yes, he's very idealistic, but he's also ridiculously SP. Lloyd lives by Se, constantly thriving on living in the moment, following physical impulses, and experiencing anything novel. You don't have to be an iNtuitive to be idealistic, which Lloyd's strong auxiliary Fi shows. As for Enneagram, 7w8 sx/so, or 8-7-3 SIP.
Colette: ENFJ. 2 so 2-7-9 SIP. Now, Colette is a better example of the archetypal idealistic NF. She's not at all attuned to the physical world around her like Lloyd is (her constant tripping comes to mind...) and has that inner Ni vision. I actually considered ENFP for her too, as she fits with many of the most famous characteristics (extremely kind, gentle, and friendly, endearingly quirky, innocently curious)
Genis: Wow, I have the exact same view on him!

I look at Genis and think "What the heck is this kid?" It's amusing how we both seem him as a strange mix of ISFJ and ENTP. There's very few characters or people that appear to walk the line between two opposite types, and it's especially strange in Genis' case since he's so young and this sort of thing usually happens when someone has developed the capacity to use all four of their functions, i.e. an older person (then again, I guess he's not actually as young as he appears). Genis has the Si/Fe sensitivity to manners and practicality, yet also the Ne/Ti creativity and critical nature. As for Enneagram, either 6w7 or 7w6, so/sp. 6-2-1 SPI. It's interesting to note that ISFJ seems to be fairly common for E 6s, while ENTP is common for 7s.
Raine: You summed up my thoughts about her perfectly. Total NT. Incidentally, after considering her type off and on for a while, I believe her to be a kind and experienced ENTJ. As you said, she's pretty balanced on the E/I but she definitely acts T dominant, and her directive approach and preference for efficiency when discussing things among the group suggest Te. She does act like an obsessed xNTP when she goes into Ruin Mode though, or when she discovers something intriguing. Enneagram is probably 5w6 sp/so, 5-1-3 PSI.
Kratos: You're description is spot on. INTJ 1w9 sp/sx 1-5-3 PIS. Kratos is awesome.
Sheena: Is tough for me to type. I initially was torn between ISFJ and ISFP, then more or less settled on ISFP after remembering how she used Fi over Fe. But it's true that she doesn't have many SP characteristics (aside from being a ninja

). I had never even considered ESTJ, but I'd say ISTJ might actually work. She's very focused on proving herself to her clan and tries to be responsible, and make up for her incident with Volt. Her Fi could be seen as a strong tertiary of the ISTJ, perhaps.

6 sp/so 6-4-1 PIS.
Zelos: ENTP IMO. He's actually quite calculating and cynical behind his witty casanova persona. I'm not sure where you're seeing the Fi, have you managed to get his scene in Flanoir?
Enneagram: 7 sx/so, though he can act like a 3w4 at times (I always confuse these) 7-3-9 SIP.
Presea: Obviously Ti dominant, though I think this might simply be a side affect of being the token Emotionless Girl rather than her real personality preference before she was implanted with the cruxis crystal. However, even after being "cured" she is still completely Ti dominant, though I don't think we ever see enough to say for sure whether she is ISTP or INTP. If there's any other function she uses it's probably Si, which could signify a dominant/tertiary loop of Ti/Si, which is the case for INTP, in fact. 5w6 or 6w5, maybe 9w1, sp. 5-1-9 PSI.
Regal: Totally. ISTJ 1w9 sp 1-5-3 PIS. The pinnacle of Stoicism (ok, after Kratos I guess). It's also interesting to note that he had a skit referring to him as the "Pinnacle of Masculinity" iirc, as well as the title "Testosterone" while being an ISTJ. ENFP males on the other hand...
Magnius: Agreed, ESTJ. 8w7 sx/so 8-7-3 SIP. He reminds me of Gaston, from Beauty and the Beast, who has characteristics of both ESTP and ESTJ.
Kvar: I'd say INTJ. 5-1-3
Rodyle: Obviously NT. It's interesting you that you say you're torn between ENTJ and INTP. Is it because he appears T dominant, or does is have to do with the shadow types? I actually saw him as more ENTP than anything, in contrast to the cold efficiency of Kvar Rodyle was more spontaneously maniacal and a "mad scientist" type of character, an archetype often attributed to ENTPs. 7w8? 3? sx/so 3-7-5
Forcystus: I must disagree here. It's possible the fact that he was one of my favorite characters is clouding my judgement, but I say he was ISTP. I can't deny however that he did use a good deal of Te. ExFJ however is way off IMO. How did he in any way use Fe? 1w9 or 5w6, sx/sp, 1-5-6 or 3.
Pronyma: Yeah, probably ESTJ. 1w2 or 8w7 sx/so 8-3-?
Yuan: To me, Yuan is one of those badass anti-villian type characters that is obviously IxTx, but seems to be either ISTP or INTJ. (Maybe the Si of ISTJs and INTPs contributes to them appearing too "inert" to be a badass leader of a rebellion?)
Actually I think Yuan is in fact INTJ, or even ENTJ. His authoritative manner and organization point to strong Te. Then again, he doesn't seem like he really has much of a well-thought out long term plan the way an INTJ would, considering how often Lloyd's group is abruptly incorporated into his plans as they appear...

Enneagram wise, 1 or 5w6, sp 1-5-3 PSI.
Botta: xSTJ 1 or 6, sp 1-6-5 PIS.
Mithos: Finally, a legitimate INFx main villian. I always liked to think of him as a broken INFP too, but functionally INFJ probably does fit slightly better... I'm really torn on this one. It's almost as if he acts more INFP as a child and INFJ as Yggdrassil. Enneagram 1w2, possibly 4? sx/sp 4-6-9 IPS.