To cast my vote on this issue, I'd like to say I find most of the proposed nerfs in this thread abhorrent.
Transports need to be good to be worth having at all. My gut reaction is the game will be less fun in a big way for me if transports are nerfed too hard. Strategic Bypass is an intended feature in this game and I'd like to see it stay. I don't want to have to slog through every last system and defense nor should I have too if the game is meant to be fun.
I know none of these ideas will be adopted as is without careful consideration and testing, I just thought I'd share my two cents for what its worth.
Transports really are far far too good: for one they shouldn't make all of the ships inside have no energy cost (was far too easy to exploit this and build past my energy cap)
I'd rather not see this changed in any form.
I never crack Z Reserves as I never have enough energy to spare for them. As things are now you could use transports to raid and store Z Reserves til you had enough energy to support them later. I'd like to try this as Z Reserves fall off my radar otherwise and I feel its a waste since I am interested in paying the trade-off to use them. (capturing Z generators is on my to-do list of things to try in this regard)
If it must be changed at all, why not have transported ships be in low power mode while they are inside?
I don't abuse transports in the way described in the above quote but this change should still allow me to steal a Z Reserve or two for future use without killing my economy permanently. Naturally I could simply leave them unbroken til I was ready but then I never get around to doing it.
Its like saving your nades or powerful items for a rainy day only to beat the game without ever using them kind of thing. If I were to break one I'd be sure to use it since it'd be right in front of me. I could also scrape afew but scraping Z ships from reserves strikes me as wasteful but perhaps its necessary