The brief history of flute scales is that the original Boehm flute was made for a lower A - something like 438. As the A slowly climbed toward 440 (or higher), tradition was stronger than engineering among flutemakers and they never repositioned the tone holes. They just made shorter head tubes. But since the head tube length affects short tube nodes (e.g. C#) more than long tube notes (e.b. Eb), this just put the flute out of tune with itself by raising some notes more than others.
In the 60s or 70s Cooper repositioned the toneholes for the higher A. His work was both theoretical (mathematically computing the best position) and empirical (tweaking position based on actual playing). The Bennett scale is a slight variation of Cooper. The only difference I notice between Cooper & Bennett is the C# vs. high D. Some manufacturers have their own modern scale, many of which are variations of Cooper scale.
I said "tradeoff" because no flute scale can be perfect, not even theoretically, because the same toneholes are used differently for different notes. Each of these different usages would want a different position or size of the same tonehole, so the size & position of the tonehole is a compromise among them.
Even if a theoretically perfect scale could be built, however, I'm not sure all flute players would like it. We get accustomed to blowing each note a certain way and it's hard to teach an old dog new tricks - especially when the dog doesn't want to learn any new tricks because he can already play in tune so there is little or no benefit to learning yet another scale.
Personally, I find that the scale of the flute makes quite a big difference. Going from a flute with a terrible scale - say a Gemeinhardt - to a Cooper or Bennett scale flute makes a WORLD of difference. The better scales make it a LOT easier to play in tune.
Some people seem less sensitive to the scale of the flute than others. The two most common reasons why that I have encountered are: (1) Some automatically adjust to it without even thinking about it so they never realize what a difference it makes. This is common among professional or highly accomplished players. or (2) Some are less sensitive to intonation and don't notice how out of tune it is. This is more common among students and beginners.
If you ever want to test out the scale of a flute there are a few key notes you can play in front of a tuning meter: middle C#, middle E, middle & high Eb, high D, high F#, highest Bb, and a few others.
Also the headjoint plays a role in the scale. The geometry - for example the rate & amount of tube taper, among other things - affects intonation. So the head should be matched to the body for ideal intonation.
Then there is the "A": 440 or 442. Most flutists find it easier to play in tune at A=440, with a flute set up for A=442. The $64k question is why. I think it has to do with the fact that the air is warmer at the head of the flute than at the foot. This difference in temperature means the speed of sound is faster at the head than at the foot. Since a flute selects a tone by wavelength (distance to tonehole), faster speed of sound means a higher frequency matches that wavelength distance. This will tend to make a flute sound sharper for the short tube notes, relative to the long tube notes. Tuning the flute to A=442 and playing it at A=440 means you have to pull out the head further to get that A=440, which flattens the short tube notes more than the long tube notes, which reverses the effect.
Now finally, to answer your question, any flute with Cooper, Bennett or a scale based on them is likely to have good intonation (assuming a good headjoint match). Yamaha used to have a poor scale but they improved that a few years back and now they are OK. Jupiter & Sonare also have a good scale.
