Regarding vanilla characters... That depends how you classify "favorite", haha. For instance, I hate Wesker both as a character and how he plays, but I play him cause I'm good with him.
I'll just go ahead with those characters I actually enjoy. And it's a BIG list, so...
Trish is just so fun to watch with her traps and huge sword. I'm totally straight for her. Favorite hyper is Round Harvest.
Arthur - I just loved Ghosts n Goblins, and he is just so fun to watch and play as. For the Princess is, of course, just perfectly fine as a badass hyper for him.
Tron actually is one of, if not my absolute, favorite characters in the Mega Man universe. She is such a fun character in the Legends games, and I think I'm one of the very few people to be able to say that they played her own solo game, Misadventures of Tron Bonne. I also just love using her cause she's so fun - and it seems I'm actually decent with her. Hyper? Well both the Level 3 and the Lunchtime ones are amazing. I can't decide!
Of course, I'm a huge sucker for
Crimson Viper, I've been trying to play her for pretty much shortly after getting the game. Favorite hyper... I don't really have one, they all look badass. But I guess Burst Time.
Then there's
Hsien-Ko, who was my main character in Darkstalkers and on my first team when picking up Mahvel. Though she is terrible in this game, I still like her very much. Fav hyper combo for her is the hammer with the morning stars.
I also got to really like
Jill, and with her I like the Uzi one. It's fun!
Spider-Man was one of my longer main characters, although I dropped him in favor of Wesker. With him, I enjoyed using Maximum Spider cause I love how he says it.
Magneto, as often as he appears, is just so fun to watch. I never really played him myself, only gave him a try. Of most top tiers, he probably is the one I don't mind seeing all the time simply because he just looks so badass. Gravity Squeeze obviously is my fave hyper.
I've always been a big fan of
She-Hulk, and in MvC, she has the same status for me as Magneto. I don't play her, but she's is SO fun to watch when being used, especially by Combofiend and the likes. My favorite hyper with Shulkie is Taking out the Trash.
Taskmaster has been a long favorite of mine in terms of character, and I was pleasantly surprised about his inclusion in Marvel. I still play him (although not as often anymore since I picked up Trish), and my favorite hyper is the arrows.
I've loved
Iron Man since I was a kid, and the recent-ish movies only underlined that badassery that is Tony Stark. The tincan is another one of those characters I can't play to save my life, but they're just a BLAST to watch. Unfortunately, this guy is really rare. I hope we'll get more Iron Action in Ultimate. I don't think I need to name the hyper here...
Out of the Avengers, though,
Thor always has been my favorite character, and I still love him because of the cheesiness of his Ye Olde English talking. He was among the 3 characters I first played when I picked up the game. His Mighty Tornado hyper is my favorite here.
Doctor Doom has been the third character on my initial roster, and was the only one who actually stayed. In the time I've played this game, I dropped many characters, and I dropped the Doctor as well, but he was the only character I regularly came back to. Now, he's been anchored as my anchor. I love all of his hypers, though Doom Time is just so fun to watch - he fucking sits down and watches you suffer.
Being a big sucker for both Cosmic Marvel and villains, obviously the next character that should be named is the
Super-Skrull. Whenever I feel random, I pick him instead of Wesker in the hopes I somehow learned to be good with him, but I'm really not. I will definitely try picking him up in Ultimate, though - he's probably one of my most favorite characters in vanilla in general. As for the hypers, I like Inferno a lot, but Death Penalty is just too good. TOO GOOD MAN TOO GOOD.
MODOK is of course the next step, and when I first heard about his inclusion in Marvel, I burst out in laughter. Especially because I was told that in a very salty manor. Being a comic fan, I obviously knew all about MODOK, and I read MODOK's Eleven (a really hilarious comic, go check it out) just shortly before the news came in. And I fucking LOVE MODOK. He's definitely my absolute favorite character in this game. His theme is funky, and he is just a blast to play - despite the fact I can't save my life playing him. My favorite hyper for him style-wise is Killer Illumination, although the Hyper Psionic Blaster is really awesome in its utilization of the Level of Understanding-mechanic.
Although I don't like the X-Men series all too much,
Phoenix was one of the earlier characters I picked up. As someone mentioned earlier, aside from the DP shenanigans, she is actually really fun to play as, and I enjoy whenever a Phoenix player has the guts to actually use her on point and not just tag her out immediately. Watching Clockwork play regular Jean is just amazing. I love Healing Field as well.
Dormammu obviously is another one of those villains, and I've always loved his badassery in the comics. While I usually am not a fan of redesigning characters, the redesign of Dormammu, which MvC uses, is one of the best redesigns ever made, and Dormammu looks just awesome. I really hope this look sticks around, because the old red spikey flamey head is a little bit silly for the evil overlord of the Dark Dimension. Aside from that, Dormammu also was one of the characters I tried playing early in my gamelife, but it should never work out. I love all of his hypers, though the Level 3 is probably the best cinematic hyper in the game, so obviously that one takes the cake.
Speaking of Dr. Strange's nemeses, there's also
Shuma-Gorath. As soon as he was released, I bought him and immediately played him. And he turned out to be really fun to play with. It also really felt that the comboing with him is extremely fluent. I never was a fan of chargers, though, because I don't get along with them, so unfortunately, I eventually dropped him again. I still love seeing him whenever I do, and of course Chaos Dimension is my favorite hyper.
Finally,
Storm, one of the very few X-Men I actually really like. She was another one of those early characters of mine, and I actually recently started slowly picking her up again. I love seeing Storm's movement and attacking, and she is really fun to watch on streams. My favorite hyper is the cinematic one that triggers DHC glitch so well, I forgot its name.