the topic of the upgrading system has been quite controversial when it has been discussed in the past. For PvE players the upgrade system presents a long term goal and an incentive to keep playing the game, however, this is different for PvP-only players. At launch the upgrade system will probably render certain decks in PvP unusable (lack of charges), essentially forcing players to grind PvE maps if they want to play their preferred deck. However, this is only one issue. As time goes on people will start to get their decks to level 100+ and everything will be fine since everyone has upgraded decks, right? Wrong. New players will have a very hard time getting into PvP since they have a low level deck, while the players who have been playing for a few months probably have a mid to high level deck. This can cause a lot of frustration and even potentially lead to them quitting the game. Personally, I think in PvP all cards should at least be U2 (if it isn't U3 already) and have two extra charges (if you don't have all three) . This keeps some kind of progression (reaching U3 with 3 charges will take just as long as before) while also immensely improving the new player experience. Additionally, at launch almost all PvP decks will be playable, due to the two extra charges. While this might not be a perfect solution, it's definitely an improvement. (The idea is from Kaliber84)
This post from LagOps also makes some good points. He also elaborates three of the change proposals from the poll.
Here are some old topics where this was discussed:
Seperate PvP from PvE
Removing upgrade system from PvP
I feel like things might go wrong
Making it hard to get all the cards and upgrades
My one issue with the BattleForge reborn project - A proposal
Why I quit battle forge, and why I miss it.
EDIT: Split the poll into two parts.