I can´t know whether Branagh´s untampered vision of THOR would have been better than the Marvel product. But I guess Marvel has shown with IRON MAN 2 that too much of their straitjacket-ing a director does not work at all.
And since opinions wildly differ, I do think that Joe Johnston was a very good choice for CAPTAIN AMERICA (somebody obviously loved his ROCKETEER). I also love SUPERMAN RETURNS and THE AMAZING SPIDER-MAN (and find SPIDERMAN 3 extremely boring).
With THE AVENGERS, however, I believe the situation was very different since Joss Whedon is a very idiosyncratic director who knows how to work around "suggestions" and "authorities". Also, he did not need THE AVENGERS like Branagh needed THOR. And Marvel was aware how difficult THE AVENGERS was to pull off. A lot, if not everything depended on that film being a success.
Making a huge ensemble work is Whedon´s specialty, so he was needed for this film. Also, he´s geek-approved. Getting him to do THE AVENGERS was a major coup. If they had bullied Whedon as much as the un-geek-approved, unbankable Branagh, Whedon would have found a way to tell the fanbase. Which would have meant: bad news for Marvel (in a time in which they already deservedly got flak by Jon Favreau who did not return to Marvel after his problems on IRON MAN 2.)
I guess Marvel knows how to market their stuff to the fanbase extremely well. Better than WB. Also, they have less worn out protagonists than WB. But I do think that Marvel is at a crucial point now. After IRON MAN 3 that character will be pretty much burnt out and only remain usable in future AVENGERS´ films. CAPTAIN AMERICA and THOR can finish their trilogies - but that´s probably the end for them, too. They could resurrect the HULK again - but that one is a very tricky character for the big screen, obviously. I hear a FANTASTIC FOUR reboot is being worked on - but they are problematic as well. All the other heroes from the Marvelverse are rather unknown (to general audiences which are needed).
And I also believe that the era of superhero movies has already reached its peak. At some point people will grow tired of them.