An imbalance arises when a characteristic of a ship can be exploited to gain an advantage over another ship. In the case of power 2.0 it is the distance requirement of stabilizers. To someone who doesn't care about distance, it can be used to gain a considerable advantage over someone who does.
Take two ships of the same length; both of these ships have the same maximum capacity for energy generation in the new system. Ship A uses 100k blocks, ship B uses 250k blocks. The player that built ship B spent more than double the resources and has the larger ship, so why wouldn't it's capability potential be more than that of the smaller ship?
If what you want is to bridge the gap between pvp and rp, then you need to do away with this dimensional based power system because, as I said, some players wont care about dimensions and use them to the detriment of players that do. The shape of a ship should never impact its performance to this extent if you want to maintain creative freedom. Players concerned with performance will build a certain shape while others that don't build that shape will be disadvantaged for not doing so.
Also, if you want to limit energy output to a given size of ship and thus limit systems filling ships, then you need to find an alternative to gauging ship size. The length or height or width of a ship is an extremely poor measure. There will be no way of balancing this because of the extraordinarily vast range of ships that players create. Instead, consider some other way of judging ship size.
If you want an inherently balanced system, then energy output needs to be tied to ship mass or ship block count. If this is done, then ship B (the larger ship) will have a higher capacity for energy output and consequently a higher capacity for offensive and defensive capabilities, which naturally should be the case anyway. Players that dedicate more resources to ship construction will then be rewarded with better ships because the "strength" of a ship is tied to those resources and not to some inconsistent variable that's easily manipulated.