From a raw numbers perspective, yeah, you don't need a governor for every planet. The planets can run fine without it. However, considering they just added the option in for individual planet governors, it's really, REALLY counterintuitive (and not fun) to say "Hey, here's this new option that you can't really take advantage of because of an arbitrary limit we're also adding in." Even if they kept the number the same but made each type of leader have their own pool (effectively multiplying your cap by 4), you'd still only end up with enough governors for each sector with maybe 1 or two extra for the powerhouse planets that already have a large population. Yes, this is presuming a huge galaxy, aka 1000 stars, but if the game has an option for a bigger galaxy then you should have options to genuinely play in that bigger galaxy without being penalized for it.
Also the argument flat out fails when it comes to scientists since the game has been designed for years around science ships requiring a scientist to man it. By saying that I CAN put a governor on each planet at the cost of having enough scientists for just the basic stuff, they're effectively saying that I can get some minor stacking boosts to some planets at the cost of engaging with a core part of the game, exploration (which includes way more than just revealing the galaxy). That kind of cost is just untenable. I MIGHT, MAYBE, play ONE, 1!!!!! game without doing (or having severely minimal) exploration at some point just to see what it's like being a true isolationist. But considering how much anomalies, archaeology sites, and all the other parts of exploration add to the game....HELL NO! That's not a play style that I'm interested in beyond a very, very short passing curiosity.
I think it's pretty clear Paradox wants to (again) nerf wide empires. This time they're bringing back a penalty they tried a while ago (leader cap), which originally didn't work as a penalty because wide empires could either steamroll the extra costs with one or two extra admin worlds, or they would just not have leaders at all since, at the time, it was widely agreed leaders were pointless as they only gave minor bonuses relative to their sprawl penalties. (Seriously: unless you went to crazy lengths to build really good leaders, on average you were only getting +10% to one specific thing by filling that oh-so-coveted leader slot.)
With leaders giving more substantial bonuses now, it makes sense that Paradox would try the leader cap penalty again. This time, apparently (if going by your own example), it seems they've managed to hit the fabled balance of
just barely penalizing wide empires by, of all things, giving them
too many options.
The argument you're trying to make, that wide empires suffer unfairly from leader cap limits, runs into a problem when we consider that the council is more valuable to wide empires than to tall ones. As you handily point out, smaller empires can afford to stuff their core sector full of governors (consider the following: single-sector technocracy with a ringworld), whereas larger empires struggle to even have a governor in every sector.
For a wide empire, the council is actually
more beneficial because it gives you a way to apply bonuses even to planets or fleets your leaders can't personally manage. Whereas, for a smaller empire, the council is
less beneficial than ecu-fying every planet in your core sector and giving each its own personal governor. The better question is how many planets (/fleets) it takes before the empire-wide bonuses of a council start to outpace the single-target bonuses of a local leader... but as long as the amount is "more than you'd need to win anyways," then it remains fairly well balanced.
So, in terms of governors/admirals at least, I don't think the new leader/council system is poorly balanced. I think it's actually a pretty good way to differentiate wide gameplay from tall gameplay by giving them different priorities (empire-wide buffs vs single-planet/fleet buffs), and a better way to differentiate military/econ/tech-focused empires by putting leader class requirements on key council seats (e.g. admiral-heavy council has better fleets but few/none tech or econ boosts; compare to before where bigger empires were better at everything by virtue of having everything). I like the change, I see it as strictly beneficial both for wide and for tall, and I honestly don't understand the criticism against it except for the issue with scientists.
As for the issue with scientists, I think all I can really say is I disagree with the argument you're trying to make because it's entirely arbitrary: you're trying to say they can't change a core feature of the game just because it's one they haven't changed before. You're saying this for
Stellaris, the game which changes core features so often you have to relearn the whole game at least twice a year. And you're saying this strictly as a matter of personal preference, which is that you don't like playing small or isolationist empires. Since it's an argument from a preference I don't share, there isn't really anything I
need to say in argument, except maybe for "yes they obviously should work on scientist roles some more, but as a hotfix the suggested course could work fine for now."