As someone in beta and someone who is an avid Marvel fan, I am also on the forums and I know what their reasoning for the "hero token" change is. In short, they want more people to buy packs and not simply buy G's to get the select few heroes they want to play.
As it stands now, just from beta testing, it appears that the top 5 most played heroes are as follows. Keep in mind that some heroes from launch are still not in the beta, so it's only a limited sample size. This is based on character feedback posting (based off of poll results only, though posting totals would give a similar result).
1. Spider Man (376)
2. Thor (261)
3. Cyclops (244)
4. Iron Man (240)
5. Storm (235-starter option)
The bottom five looks like this, however.
5. Wolverine (165)
4. Punisher (142)
3. Captain America (140)
2. Black Widow (101)
1. Black Panther (96)
You look at that differential between the most played character currently in beta and the least played. That's bordering four TIMES the playtime of Spider Man to Black Panther. Now Gazillion put time, money, and effort into both of these characters...so why is nobody playing Black Panther? It's a waste of resources to make one of the most iconic members of the Avengers?
So now Gazillion is faced with a situation. It seems very few people "like" Black Panther, for whatever reason. They would either have to a. give incentive to players to play Black Panther by making him so cheap he's practically free, b. make the cost of Spider Man so extreme that he's not four times more played than Black Panther simply because he would cost so much, or c. scrap the wasted time and effort they put into Black Panther and attempt to place a new hero into the game, starting from scratch.
So, what do they do? Those options all seem dreadful and not intelligent from a business perspective. Instead, they give you more reason to want to buy packs by ensuring that you're not 100% guaranteed to get the select few heroes you want from the store, while at the same time giving the casual player who don't wish to spend a lot of money (or perhaps even any money at all) on the game the chance to get characters like Thor and Iron Man and Spidey at higher than a 0.01% drop chance off of bosses only.
I will admit that they system needs tweaking (the chance to get new heroes from dropped tokens should remain, but if you buy a token with G's depending on what tokens will cost I think it should have a higher guarantee of giving you a new character). As I currently stand I will begin the game with at least four heroes (Thing, Cable, Cyclops, and Jean Grey), and before the game goes live I intend to buy with G's at least one more (I will definitely buy Human Torch). However, one thing that the token does do is it "equalizes" the cost of each hero, meaning that they don't have to put such massive gaps in the prices of characters simply because they are "fan favorites". Think of it in a different spectrum. Imagine if you went to McDonalds and had an option of a Big Mac or a DQPwC. Both are the same weight, have the same ingredients, ect...but the Big Mac is like $5.50 while the DQPwC is like $1.50 simply because way more people buy Big Macs. It's the same as it stands now with the in-game store. Besides which, the token system also gives more justification for all of the premium packs to have the same cost, because now heroes cost the same amount.
I see the reasoning behind the change, but I will not disagree that it needs modification. Overall, it makes sense from their perspective. However, since when can the players ever see things from the perspective of the game developers.