I had no problem with the aliens thing in Crystal Skull - it's certainly no sillier than the wrath of god in a box melting the Nazis faces. The movie has several major flaws (too many protagonists to develop properly, unnecessary CGI animals), but the aliens didn't bother me at all. The films have always been about thoroughly implausible maguffins.

As a fanedit, I think it needs a "light touch" - tightening here and there, sorting the colours and removing the odd redudant CGI critter or lame 'nut shot' joke, rather than the radical changes proposed.

But it's all about personal taste, I guess.