If I remember correctly Energy cost was supposed to limit the amount of Mark V Turrets the player could build. So their Energy cost could be doubled or increased by 75% or 50%.
It does add up. In many of my games, I'll end up running 40-50 matter coverters at endgame, just to power my Core Turrets that I've built everywhere. That's 4000-5000 m/c per second. Aka, most of my endgame economy.
I love the dang Mk5 Turrets, but I think it may be too OP...I mean, last few games when I capture sufficient number of Turret Controllers I just replace ALL of my normal turrets with Mk5 due to the fact that full cap of them is around 2.5 times stronger than Mk1, and you need to spend knowledge to get mk2 AND build that to cap and at least half of mk1 to get to the same effectiveness level...and only on a single planet. I really think it should get some kind of nerf...
While you're correct that the Core Turrets basically replace Mk Is, there's the question of exactly how powerful should they be? You need to first find, and then capture/hack a specific Fabricator to get each turret type. Getting all 8 costs either 160 AIP or 985 HaP - neither trivial.
One of the reasons they seem so powerful is that they can replace Mk I turrets everywhere, and Mk IIs everywhere but your one whipping boy. They do a decent to good job of stopping low AIP (<100) waves if you've got 3-4 useful types. However, even en masse, CPAs will crush a system with nothing but Core Turrets, and Counter Waves will frequently cause problems as well. So they cannot be relied upon as your only defense.
This falls back to the old discussions of distributed vs concentrated defense. Whipping boys and blockages and low-interconnection maps became the standard for play at high levels, because that was the only practical play style. The introductions of Core Turrets has allowed higher difficulty play on wide open maps, as you can actually defend more than one or two systems. I've been enjoying the Hex map a lot, for example, which I would have never touched before.
So if the distributed defense has become too powerful when centered on Core Turrets, what about reversing the situation? Allow normal (Mk I-III) turrets to have half-caps on a per-planet level, and Core Turrets to have a full cap, galaxy wide. It'd encourage spending Knowledge on normal turrets more frequently, give a better reward for doing so, while still giving something out there to really power up the Whipping Boy system for dealing with Exowaves, CPAs, and the like.
Would probably require rebalancing K/energy/resource costs.