I don’t know as much as a lot of the people that post here, but I’ll try to help with what I can.
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The characters to put together is very dependent on the situation, really. If you’re doing PvP, putting characters together that play well off each other (Using Iron Fist’s 
power to generate black tiles for Hulkbuster Iron Man to use his own heavy-hitting powers, for instance). For PvE, using characters that help to control goon enemies countdown tiles works as well (like Falcon’s abilities to disrupt enemy tiles or Original Black Widow to extend the enemy countdown timers, etc). Half of the strategy is finding out what works and what doesn’t. PvE is a good way to test different combinations or through the Shield Simulator in PvP.
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There are currently four versions of Wolverine: Two-star Astonishing X-Men, three-star Patch Wolverine, four-star X-Force Wolverine, and Five-Star Old Man Logan (five, if you count X-23 as the “All-New Wolverine”). All of their set ups and powers are all different and most quite usable in their respective star range. There are currently two versions of Thor, 2-star Marvel NOW Thor and three-star Modern Thor (again, if you count the four-star Goddess of Thunder Thor, it’s three versions). Both characters have the same powers, but their damage output is top-notch for their ranks, so they are very popular characters for players going through the two and three star period of the game.
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Any character you enjoy playing with, really. Some popular and useful characters include Hulkbuster Iron Man, Ice Man, Jean Grey (four-star and five-star Phoenix), Cyclops (both three and four-star versions), Iron Fist, Professor X, Silver Surfer, and Luke Cage. The list doesn’t end there, but those are names that are thrown around quite a bit here.
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As you get further along in the game, a lot of the lower ranked characters are pretty useless. Judging from your roster you posted, any one and most two star characters aren’t really needed. Some of the least popular three and four star characters are Gamora, Star-Lord, Vision, Elektra, Invisible Woman, Mr. Fantastic, Quicksilver, and Ragnorok.
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The Deadpool Daily is absolutely worth the time. It is a consistent way to earn ISO and three-star character covers. Having one-star characters for the one-star node will give you a chance to earn 500 ISO. Not super important, but every little bit helps. If you have the required three-star character for that day and complete that node, you move on to The Big Enchilada mission, where you face four waves of enemies with one team. Once you complete it, you get a cover for the required character of the day. You can also earn “taco tokens”, which you can use in the vault to earn other covers, ISO, Hero Points, or extra Health packs. It is the easiest way to build reliable three-star rosters. Overall, each day, you have the potential to earn a three-star character cover, two tokens for the vault, and 3,750 ISO (provided you have one and two-star characters and the required three-star character for the day).
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Unfortunately, I can’t answer this question. The alliance I roll with consists of my real-life friends, so we don’t really worry too much about placing high or anything like that.
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Honestly, you’re better off using Hero Points on roster slots. You have the potential to earn covers either randomly or through events, but roster slots will always cost points. If you need to, you’re probably better off purchasing characters from the other storefronts (like for the current PvE or PvP event is happening at that time). Heroic has a generally fixed drop rate, but the others will have featured characters that have the potential for higher chance at being picked. You can click on the little question mark button on each screen and it will give you the percentage for the drop-rate based on which package you buy (single token, 10-pack, or 40-pack). Each one is generally “on-sale” at different times too, which probably explains the different costs.
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A little of both, but probably mostly the former. Once you have a single cover in a power for a character, you can pay hero points (i.e. real money) to purchase additional covers for that power, thus maxing out the character without having to wait until you get 13 covers through events or drops. Since Silver Surfer and Phoenix are still relatively new characters with a high rarity rate, the ones you saw were most likely increased with real money.
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I always liked Hulk and Classic Magneto together, but some more hard-core players will probably give some better strategies. I recommend reading through the top stickied thread of this forum, the character ranking guide. It is great for reading about potential combinations and strategies. Some of the information may be a bit outdated now, but it is still worth reading. (Or you can just click here: https://forums.505go.com/discussion/29852 ).
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The three characters that other players face in PvP are the last three characters you won a match with, from what I understand. So if you won with Silver Surfer, Phoenix, and Hulk, those are the three characters others will face. But if you switch it up to let’s say Magneto, Thor, and Star-Lord, go into a match and lose, the team other people will face will still be Silver Surfer, Phoenix, and Hulk until you win again with a different combination.
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A character’s max level is dependent on their star ranking. One-star characters max out at either level 40 or 50 (depending on how many powers that character has), two-stars at 94, three-stars at 166, four-stars at 270, and five-stars at 450.
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The crystals signify that the character is buffed and made stronger for the event it is in. Every week, the developers buff a few characters in each rank for all events while each event (PvP and PvE) have their own buffed characters. Typically for PvP, it’s characters that are the running theme for that event. For instance, a PvP event centered around the X-Men will have a number of characters like Cyclops, Wolverine, Storm, etc buffed, while an event centered around villains may have characters like Dr. Doom, Magneto, and Kingpin buffed. The increased level, like the Kingpin example you mentioned, is what level the character fights at while buffed, so their HP is higher, their attacks are stronger, and their powers do more damage.
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The buffs depend on the event. Every week, the developers buff a certain number of characters. The easiest way to find out which ones are to go check out the Patch Notes topic, stickied at the top the General Discussion forum.
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In this case, the players have picked three characters that are buffed for that event. It makes sense, since having three characters that are much stronger makes them harder to defeat. Any time you enter an event, the game gives you a list of which characters are buffed for it. So all you have to do is pick characters from that list, provided you have them, of course.
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Probably because getting punched in the face by Hulk can only do so much for your rugged good looks, I suppose.
