The sorta jazzy motif for the Main Menu might've made for a pretty decent fighter theme. I kind of get the feel of a nightclub or something of the sort. I love the part that begins at 0:51, though I'm not as sold on the transition to that part. I'm not sure how well it would've stood up as an actual menu theme, but I still like it as a stand-alone theme independent of intended context.
The character select theme also works as a short ditty to get the players pumped into action. You hit the target here, and style-wise it does feel consistent with the main theme by my meager understanding of musical genres, instrument names, or what have you. I'd look into reusing this one again in some context if you can.
The tutorial mode is very relaxed, and the bird noises do make me wonder if this was intended to be a Ferdielance-related thing. The singing voices feel like they don't really fit here, like they're a runaway set of voices desperately seeking a climactic battle theme but are trapped in the company of peaceful chirping birds. As a tutorial theme I could see this being passable as the basic training room stage music too.
The Generic Arena has a great introduction part, but after :30 or so it feels like it runs on empty for the rest of the track. It seems unfinished, but the basic idea of what you have here has a lot of potential.
GiGi's theme is very good. It gets kicking at the right time, and the melody is easy for me to follow although it seems a bit mellow for my mental image of the Justice Riders. The more subdued nature is really the only thing that works against this in my eyes (ears).
Having played one of the cases he appears in, I really like the more dangerous atmosphere that this theme puts forth. I do get a very good sense of a danger that's hard to pin down - you know this guy is bad, you know he probably did it, how? It is conveyed well in spite of the instrumentation and composition that often feel discordant and a bit harsh and jumpy.
Michio's opening is very strange, suggesting he's off-kilter when he was one of the more emotionally stable characters of 0.1, though the slow opening may suggest something of a quieter strength he has (this part I liked the most). When the theme gets going (it is very slow to start), its tone feels like it jumps around everywhere, further away and sometimes suggesting to me an undercurrent of fear and uncontrollable circumstance into the unknown. It might be sort of true to a paranormal investigator on the surface, but I don't know if it encompasses him well.
I do not know of Cal DeCurrens at all, but the theme kind of makes me think of the far east a lot. This is one of the tunes where I think you get the pace and energy of a typical fighting game stage theme about right. I wish I could say more about this. Maybe it's not the deepest melody of the lot, but it works just fine for me - it's very listenable.
Isis has an amazing theme. It does sound like someone remixed a trainer battle theme from one of the games, kind of reminds me of the DS era. You captured the spirit of that very well! It's energetic and upbeat, which admittedly Isis herself as a character doesn't quite come off as - but it matches the environment she comes from. Composition-wise this is great stuff, moving quickly with confidence and feeling very 'Pokemon but not quite.' It has my vote as one of the best of your efforts. (Dinner is serving... you.)
Ryuuma has that borderline problem with slow, but I love the transition from quiet and introspective to utterly chaotic in 0:15 - I think you manage this change in moods a lot better here than you do with Michio. I remember Ryuuma having a severe lack of control of the situation in spite of the expected tropes of a master chess player, how the melody moves towards suggesting he's about to have control but then the bass just creeps up and throws it all back into chaos. This is a keeper to me, just a step below Isis.
Alnar's theme comes off to me more as an amazing platforming level theme for a great open plain, but it has that undercurrent of whimsical behavior underneath it which has a very sinister transition into something that suggests a lot more to whatever's going on... but I'm not sure if both halves really come together. The first half I rather like a lot, though.
Got's theme is definitely more in line with how I would've seen a JR level theme, which may well be why he gets this one. It's very bold, actiony, charging head-first into danger in order to go save the day! How that lines up with Got the person, can't say, but I'd say he made off with one of the better themes. It gets to the point, the melody evolves in ways I find enjoyable, and I wouldn't mind listening to this on repeat if I were in the Justice Riders game myself. This is certified a fine fighting game theme.
GuardianDreamer got probably the best initial set of notes, but then it doesn't seem like it can decide if it wants to be an early FF or Pokemon-style battle theme. I'd say it hits the intensity of the genre's action just right. Maybe some of it really could've escaped into an optimistic Fire Emblem battle theme that suggests a level of cautious introspection about the scenario around them. It's still a good all-around theme.
Sleuth's Jaws theme opening as a reference to their love of sharks is pretty nice, though the intro is very slow and doesn't get going until way too long. The guitar arrangement on top of the sinister jaws notes kind of paints them in an oddly villainous light which I don't know necessarily fits them well. It is pretty catchy as its own thing and the loop gets back into the actual music mercifully quickly so I don't have to sit through the empty sounding bass for too long.
For Blackrune, I'd have gotten to the organs right from the word 'go.' Things admittedly feel like they almost fall apart around :30 with the weak transition. While they don't always come together well, the guitar and organ combination does suggest this man is trouble on some level! It casts an air of some sort of dusty, evil place of unfathomable consequence, even mysterious but not standing to linger around and search for clues... but to get acting. It's uneven, but not bad.
kwando got a more subdued and elegant theme that stands as very different from most of the cast. I feel the melody definitely takes a dive around :53, somehow I don't feel the trumpets bring the whole thing together that well, but the rest of it is pretty good even though it is rather mellow. Given their favorite genres, I would argue that for the most part you hit the mark and this stands out as something listenable although I'm on the fence about it as a fighting game theme.
DWaM's depiction as being all about the grim, darkest depths of everything lends itself well to the very slow build-up, I'd say this is an instance where this works. Once it kicks in, you get the idea that nothing good is going to come out of this. It's very characterful. The lyrics are hilarious and somehow manage to simultaneously ruin and solidify the theme. It's not as intense as what Blackrune has, but it feels more even overall despite the voice bits not completely feeling in step with the rest of it.
Higami has that slow start problem, but it picks up to something stand-out at :32. I like the choice of instrumentation a lot. The discordant composition, how just almost everything feels off by one note here and there, leading to that quiet introspective part with the piano matches his crazy personality very well. The rapid pace suggests he is in pursuit of something or another, imagined or otherwise. All suspicious and strange, befitting of his character personality and role in his game's story. It's a good fit.
Was Unas intended to be the final boss? Tone-wise it's very hard to see this as that. The beginning makes it feel like more of a bonus stage theme, then it continues on to a melody that doesn't catch to me much up until about 1:16 or so where I can feel an upturn of something menacing. This one feels like the biggest miss of the lot, but it probably would work well as an early level theme in a different game genre.
I like the first jingle, the way the typical failure jingle trails off as though it were to fall off a cliff into oblivion. The got/GiGi jingle doesn't feel as distinctive in turn, sadly.
Saving Teruko for last - seeing Sleuth and yourself say they're favorites that made me feel like maybe I should be saving it for last - this one is an incredible finale for listening to the OST. I think it hits the pacing for a fighting game BGM just right, and the choice of instrumentation and tempo changes lend to the idea of strange swings in tone and making it kind of hard to pinpoint what exactly is going on with them. It's exactly appropriate to her character. I'd love to go into more detail here, but it is very significant spoilers for a game still going.
In short, your top three are, if I had to really pick... Isis, Teruko, and Got. Ryuuma and GD come very close. A lot of these are nice, so it is hard.