There are a thousand ways to 'skin a cat' in the aviation world.
There are large FBO's, small "mom & pop" schools, flight academies, collegiate aviation, the military, etc.
Which way is the best way? Personally, I think the US military "Undergraduate Pilot Training" because the price is right and you're going to fly way cooler things than you'll ever have a chance to in the civilian sector. Plus, you'll be a 'known quantity' candidate and you can pretty much write your own ticket in the aviation world when there's hiring going on.
It depends on the student. Some students will thrive in a small FBO environment, some other students have the resources and desire to go to a flight academy.
Which is better?
Neither.
Flight academies are a lot of money, FBO's have far lower costs and lower prices. Some flight academies offer CL-65 prep... You don't need it, the airlines don't require it, but if it's something you're interested in and want to do, go for it if you've got the financial resources. The multi-engine rating I earned at ERAU was the same multi-engine rating that I could have earned at Falcon Air for a lot less.
However both environments offer different tools to different students.
A couple examples. I'm a big fan of ATP, but ATP isn't for a casual student who likes to be spoonfed and coddled like a child. The student has to arrive prepared, motivated and ready to learn or they're going to whip his ass and then he's going to show up on the forum later complaining about he got cheated out of two extra hours of extra training in the Seminole where in fact he came to training flights unprepared on several occasions.
I'm a 5-year ERAU grad. It was a lot of money, I spent a lot of time and cash doing things that amounted to more or less dumping hoardes of cash into a roaring fire.
Would I go to ERAU again? No, but considering the networking contacts, the people I met and friends that I made, I'd certainly at least hang out there on the weekends and sponge sponge sponge.
If I had stayed in Tulare and trained at the (now defunct) Gryphon School of Aviation (where I got my private), I wouldn't have met Mike Lewis/Copaman, MikeD, Joe E (not a member of the website), Bogberto, Craig Funk, Art Draut, Fred Cone, etc -- all of the people that helped me get to where I am today in their own ways.
Yeah, I complained about Riddle, spoke of the Riddle run-a-round, and I still do, but I still stayed. Looking back, considering I was pretty wet behind the ears and largely immature, it actually worked for me. I didn't have the support network that you guys enjoy. My only contact with an actual pilot was my high school counselor's husband who was an out of work four-timed furloughed Inland Empire Airlines metroliner FO who more or less told me to "...run, don't walk, away from this field, but I can answer a couple of questions".
So knowing what I know now, would I go back to ERAU? No.
But would I be where I am today not meeting the aforementioned people? Probably not.
Catch-22.
...
Flight training is 'transporation' of sorts.
There are Hondas and Acuras.
They're both cars. They'll both drive 65 mph on highway 101 with safety, efficiency and comfort.
Some folks might want leather seats.
Some folks might want cloth seats.
Acuras have some built-in features that Hondas drivers don't see or have a need for. Is the Acura a waste of money? Maybe, maybe not. Both brands have what you need however, the brands present a different product.
I live in Arizona. I may not need the heated leather seats that come standard in the Acura, but the Acura driver who spent more for the heated leather seats isn't necessarily a dumbass, especially if he lives in Michigan.