The "realistic" debate is a bit silly on both sides... Rambo taking on an entire guerilla camp is unrealistic, the structural integrity of the Starship Enterprise is unrealistic. However... the notion that Rambo is a highly trained Green Beret, hardenned on the battle field of Viet Nam, who is fully aware of his enemies capabilities and numbers... allows us to suspend our disbelief that one guy can take on a small army. The futuristic nature of Star Trek and the over the top technology depicted therein, allows us to suspend our disbelief about the design of the Enterprise being able retain its form (most people who are not familiar with structural engineering would not even question it).
And that is what it is all about... Suspension of disbelief. Audiences are pretty sophisticated these days, and they want some way of accepting what is happenning on screen. This is why Zombie movies try to give some kind of psedo-scientific explanation as to why the zombies are rising (strange gas, or virus). It is why they film movies on location, rather than with cardboard sets. To add authenticity, and plausibility when needed (sets shots are used all the time of course, but so are locations, when the situation calls for it).
Now, aliens can be made plausible in a movie about aliens... Super beings can be plausible in a movie about super beings... however, I think it is a legitimate concern that too many genres, too fast, can weaken the movie's ability to suspend disbelief in its viewers. Cap, IM, Hulk, Thor, Avengers, etc... has to build a strong track record before addtitional Sci-Fi elements like Aliens, Time Travel, Ray Guns, Light Speed, etc should be introduced. Baby steps... I agreed that Thor poses a unique challenge, but I think they will fold it all together nicely. I just don't want to see it over done to quickly.