Energy is definitely not meaningless. Late-game fleets take up a ton of energy maintenance and I've felt the crunch plenty of times before. At the very least, more energy production means less tiles spent producing energy and more on stuff you really want.
Meaningless in the sense that it's very hard to not have a complete and total glut of energy surplus, even without a dyson sphere. Late-game you've got even less energy concerns, from repeatable tech & federation fleets having no maintenance
As a organic empire I've never really experienced the 'leaders never die' thing but you're probably right on that point. I see your point on habitability too. While unity is impossible not to accumulate, having the bonus is nice for filling out the rest of your traditions while still expanding aggressively. Unless you really prioritize it in the early game or play tall it helps into the late game.
I think most states are fine unity-wise, with late-game unity being a major problem in its uselessness. You can't mix or reset ascension perks, or spend your unity in any other meaningful way. Even aggressive expanders can greatly increase their unity with domination and expansion traditions, it's pretty hard not to snowball unity unless you are RPing a super-slaver Empire. Also yeah, leaders die every century or so, so much so that it's pretty hard to notice their loss - especially when the life extension tech comes into being. As there's not much else to spend society research points late game, they become practically immortal
Consuming organic food is strictly worse to consuming energy. Unless I'm missing something Paradise Gardens/Domes only provide 4 food which is definitely not enough to feed an entire planet, let alone an empire. So organic empires still have to waste tiles on inefficient farms to feed their pops.
Hydroponics lvl IV feed 1 organic pop for 0.5 energy, Power plant lvl IV feed 1 synthetic pop for 1 energy. Paradise domes are incomparably good, because at base they feed 1 organic pop for 0.5 energy, but the additional 2 unity and the +5% happiness makes it so that they increase the productivity of the entire planet and more than pay themselves off!
That's also not if you factor in technology & the tiles themselves - not all tiles are equal. Barring the odd planet of +3 food on a tile or other modifications, most will have at least 1 tile with 2 food. Paradise dome will then give 6 food, 2 unity and +5% happiness. The happiness will increase the productivity of the entire planet, paying itself well off and beyond its 2 energy cost (moving you towards the holy grail of +20% productivity in everything from happiness). Then you've got to factor in nutrient replication giving +15% food as a T3 tech, of which there is no energy equivalent, or of the nutrient replication tech using cheap soc points in the late game, you start off with hydroponics and paradise domes being more efficient at supplying organics than power plants synthetics and end up with even better efficiency - without factoring in slaves, agrarian pops or the like.
Food accelerating growth is also far less powerful than you think it is. Synths have fixed build times (reduced by roughly a quarter thanks to Synthetic Evolution). Organic pops have growth times that scale exponentially with the number of pops on a planet. Under optimal circumstances organic pops can grow faster than synthetic ones but optimal circumstances are definitely not realistic in a game. Besides having 100% habitability on all planets with growing pops, you need to maintain a food surplus of 20+ per growing pop. That's a massive waste of resources for such a minor bonus. Realistically a synth pop is going to grow faster than an organic one unless there's less than 5 pops on the planet already.
Optimal circumstances are incredibly easy to surpass or abuse in game, as you can easily populate your planets early game, mid game & late game all limits get thrown out the window as you can convert cheap society points into food & so, into population growth. With adaptive engineering, genetic engineering, genetic diversity and the habitability techs, habitability is a non-issue especially with the nerf to habitability. To make matters even more lop-sided, organics can grow multiple pops per species per planet, with migration allowing them to efficiently redistribute their pops in accordance with the most efficient planetary growth automatically. Smaller planets produce organic pops quickly, sending their pops off to larger planets - giving larger planets the population growth from the smaller planets. This is made even better when you consider that the formula was changed to make the food growth bonus even more powerful, so that it doesn't matter how many planets or pops you have, so much as how many planets are growing pops. With absolutely minimal oversight and no rapid-breeding traits, technology or ascension perks, even a fanatic xenophobe Empire could outgrow a synthetic Empire with internal migration & food surplus alone.
Couple that with DLC and habitats? Sheeeit, 100% base habitability size 12, spam them on every orbital facility? You populate a whole ringworld in the time it takes to migrate the first generation
To be fair, I'm talking strictly about how going full synthetic is better than staying as cyborgs. You can't take the evolutionary or psionic paths if you've already taken 'The Flesh is Weak' so I haven't been counting the bonuses they provide. Going psionic and building synths is probably the best ascension path now that spiritualistic pops are slightly less pissy about robots. Evolutionary ascension is still 'Do you want to do a ton of micromanagement for your bonuses? No? Fuck you' however, which is why I never pick it unless I have to.
Evolutionary imo is one of the most powerful still (and not just because it's one of only three, it is standalone, very powerful), and its micromanaging is a lot easier if you create specialized planets & have an authoritarian ethos. Basically gives you as the player maximum control over every pop and maximum optimization over everything, even better if you emigrate some of your pops to psionics and get psionic pops that way through the shroud event. Also you can nerve staple all your foes lmao
I fully agree with you on this point. Some of the stuff teased by the Devs definitely goes in the right direction for the next patch but I'm still not 100% certain it's enough. I've tried modding in my own traits/civics/whatever before but gave up in frustration. It's not super difficult, but documentation is sparse and I had troubles getting everything to work properly.
There are some good mods on steam that do this stuff as well, though I don't use them so I can't be more helpful :[