I’ve currently got the following 4*s either rostered or waiting in line, but only 9 roster spots…Who do I keep?
Mr Fantastic: 1 blue, 1 yellow
Ghost Rider: 1 red, 1 black
Cloak & Dagger: 1 black
Lockjaw: 1 yellow
Professor X: 1 blue
Quake: 1 green
Spider-Woman: 1 red
Thing: 1 yellow
Wolverine: 1 black
Mordo: 1 blue
Nightcrawler: 2 blue
The Hulk: 1 black
Sandman: 1 purple
Gamora: 1 blue
Rogue: 1 green
You might want to slow down on opening LTs and spending CP to get 4s until you actually have more than four 3s max leveled and/or champed. You probably won’t have the ISO to level them both, and putting ISO into your 3*s right now will get you a much better return on your investment.
I don’t think it matters that much which ones you keep or sell, since the 1-2 covers won’t make much difference in the long run, and none of them are any good at only 1-2 covers. Totally pointless to sell a 1-cover 4* just to roster another 1-cover 4*, pretty much no matter who it is.
Takeaway advice: don’t open any LTs or buy any classic tokens unless you actually have an empty roster slot or the hero points to buy one. Don’t spend HP on anything but roster slots, unless you’ll still have enough to buy a roster slot afterwards (and even then, you’re probably still better off just saving for the next roster slot after that.)
I haven’t opened any LTs or spent any CP yet, these 4*s are all from Heroic tokens…but thanks 
OK; I was going to repeat @Jaedenkaal 's advice, but I don’t have to
In general, if you’re going to roster 1 cover 4* characters, you might as well roster the ones you’re most likely to get more of over the coming weeks/months. From your list that would be:
Cloak&Dagger, Lockjaw, Mordo, Nightcrawler, Sandman, Gamora and Rouge. They’re all in the last 12 4* released and have increased draw-odds from tokens (well, Nightcrawler isn’t in tokens yet, but will be after the next season starts in a couple of weeks). I think Mordo will be dropping off that list soon, with C&D shortly thereafter.
Other than that, just keep the ones you like and be comfortable in the knowledge you have a head start on them when you need it.
Your list also includes Hulk; since there isn’t a 4* hulk, is this the 5*? Hulk is probably the bottom of the barrel 5*, but I would roster him anyway… With the supposed 4* Hulk coming, maybe they’ll rework the 5*.
Ah, an embarrassment of riches then, fair enough.
At this point, all I can offer is; keep the ones you like for personal reasons, and sell the ones you don’t have room for. Exception: keep the 4* that’s required in the current story (if you have it) and in the next (Gamora, in this case) so that you can play the missions in which they are required a couple of times.
There is, actually, and he’s Totally Awesome. 
Crap; forgot Cho. I like him, but he’s not on the latest 12.
Good luck.
Thanks for the advice!
As far as dropping out of the 12 latest, I have the order as Mordo, Coulson, Hobofist and then Cloak&Dagger