You are absolutely right about a lot of things. (There's a 'but' coming, of course.) The worthlessness of early game sectors is indeed a problem that makes the opening feel stale, and also encourage energy sector spam even on sectors that don't make sense. Pre-update, aquatic sectors need 10 turns to make back their production cost in other yields, and land sectors need an amazing 30 (20 if you also produce the first sector upgrade). This is the problem they are trying to fix here by boosting the power of sectors at the start of the game. But does this end goal really have to be achieved by cheapening the late-game city planning?
Why, instead of boosting the power of level 1 sectors, should the sectors start at level 3 instead? That significantly reduces the amount of improvement you can do during the course of the game, and fails to differentiate players which took the effort to plan and develop their cities, and ones that don't. The difference between a sector on turn 3, and one on turn 50 is... 10 more yields. Just 50% more, and 2 more slots.
The food/production << energy/research issue is a bit more prickly. I intend to agree, but my reasons are different. Sectors of different types are numerically identical, you'd expect that the choice between them should be relatively balanced and a difficult consideration. For production, this isn't the case (by far) because the city center has 60 production innately, for free. Any extra production you make will look comparatively small next to this, and next to energy, which the city doesn't produce by default. Not only that, the costs of all units and buildings are balanced around that 60 free production! So any extra production you tack on will be a drop in the bucket compared to those inflated production costs.
For food, the city center also gives you 20 for free. It isn't as much as production, but the catch is that food is never your end goal. Food gets you more pop, which gets you more sectors, but to sacrifice a sector now for another sector later is counterproductive, so food sectors are mostly a no-go. You can't get 2 extra sectors out of it, because zero-food, zero-water cities are plenty capable of making it to 3 sectors on their own, so the most you can get is one sector. This goes for both the old and new systems, so I'm not going to go further on that.
Thing is the extra pops, too, are basically worthless without per-worker buffs. Each worker consumes 4 resources, and produces 5. A net change of +1 is pretty much nothing, instead of using workers to make and maintain more workers (i.e. putting them on food and happiness), just put them to work on useful things. The new system locks you into +1 forever, whereas the old one let you go up to +5 with 2 lv4 sectors, and potentially more from terrain buildings like wind farms.
So I could argue that under the new system, investing into food is even less useful than before. If you make a food sector, you gain the 4th sector that merely replaces your 'wasted' food sector. If you put workers on food, they very barely outpace their own consumption (1 food worker/1 happiness worker yield 5 food/5 happiness and eat 4 food/4 happiness).
If you want to see more food and production sectors (and workers), cities' free yields need to be toned down a lot (maybe 10 food, 20 production) and the costs rebalanced around the new, lower yields. Then, workers need to give 7-8 yields of their resource baseline (the 4 main ones at least, maybe not happiness), so that they can outpace their upkeep, and so that having more of them actually does something. Per-worker buffs from sector level should also come back so that workers remain relevant as their sectors become more powerful.
Ultimately for as silly as lategame cities could get, it took so long to get there that putting your resources towards short term bonuses would have a higher economic yield for the majority of the game anyway (even on larger maps, if you were fighting multiple opponents blitzing your nearest neighbor and taking their cities will always give you more econ than spending 80 turns building your super city).
In the new economy the decision of which sector to take will actually be a decision worth making if you're optimizing your gameplay (if you arent, feel free to play exactly as you did before I assure you it will be just as effective and be very similar).
I feel like you are making some wrong assumptions here. (Pre-update) Even if you heavily prioritise econ upgrades over units, maxing a city won't take 80 turns, more like 60, and most of the 60 turns were spent waiting for research, not actually building upgrades, which means the city was still being useful in the meantime. You aren't just beelining econ and never making use of the buff city until you hit max. Plus, most of the synergies come online at level 4 which can be achieved with T6 research, meaning turn 40 or so on normal speed.
Blitzing your neighbour isn't always a good option, if there are oceans/mountains between you, you are simply too far to walk, or if a third player is waiting for that to happen. Or if the race matchup isn't good for your core units. (e.g. Indentured attacking into a human Assembly player who then puts arc retaliation on their scavs, that's a bad day right there.) Or if it's a very hard AI and they have triple your army fully modded by the time you reach there. And there is always the chance you fail for any reason and be completely crippled.
Also, I don't know why you would assume I don't optimize, considering both my previous posts were about the update having removed the way to extensively minmax city planning. Unless by 'optimizing' you mean ignoring econ for the most part and just throwing more cities and more core units.
By the way, to everyone I've replied to, sorry for the long posts. I get excited when people engage with me (without being toxic), even if you aren't agreeing.