1. It has been 30 years since the Borg was last seen, Starfleet is stronger than before.
2. The attack made during Endgame set the Borg back 30 years, which means that if you take that into account, the Borg we are facing now have just reached the technological point they where back during the late TNG-era. Which means that while the Federation has gotten stronger, the Borg has just healed themselves from that battle. So Starfleet has technically passed the Borg.
I would like to see them be able to adapt to our weaponry (as a resist buff).
Who's to say that they would follow the same technological pathline as the did before? They may have progressed even further in those years, even exponentially. So trying to reason like that is a flat logical fallacy IMHO. That being said, I would hardly say they have 'technically' passed the borg.
Some things have to be changed to make the game playable. If one Cube could take on a whole fleet, then you'd have no chance. Likewise, your Galaxy-X Dreadnought can not one-hit a Negh'Var.
You're looking at that like it's an issue. A cube can easily be made into a 'fleet combat action' where as spheres and other 'low tier ships' could be normal vessels. While not exactly canon, the idea still works. Not everything needs to be soloable, IMHO.