Influence of Upgrades are to big?

[Vomitus]

I think the only unbalance here is a Factory price. Its 3500 now (right?..) so its rly cheap. It should be like 4500 at least.

Making it cost 4500 instead of 3500 wont make any bug difference if one player only stands on a base and buys factories/grades.
And as I see it - it is not so overpowered as you think. I was several times flooded by this tactic but it happened only those times when my team was critically lame to counter and enemy's team was all about pro. If your team playes normal/good - you'll be able to set your own factories, defend them and push enemies out of yours. If not - you'd lose even if enemy had no factories at all.