I thought the originals were "excellent" - Crystal Skull - "good". I do like them all, but CS could have been made better for sure.
I think CS/the alien theme could have been better by fans of the original (especially Raiders fans), if the movie had taken a more serious, darker tone. Slapstick and aliens is a bit too light in comparison. I did enjoy the humour, but there was a bit too much. The movie actually had a good darker scene, when Irina was explaining the skull's powers she desired as the lighting shone menacingly across her face from behind her as Indy stared at the school. However, the film decided then not to really act upon that tone it just set. Sure, we want some crazy action and a bit of humour in the movie, but there was a bit too much in the end. I also think if aliens were used at the end still, CS haters may have accepted it somewhat if it was just some sort of shadowy figure in dark lighting dishing out its punishment as opposed to seeing it in full.
As for Indy 5s direction. Though I don't think Indy's franchise has been ruined, it could be redeemed for those that feel it has been ruined, if they just simply did as above. Make it darker, more mysterious, like the originals. Sure, TOD and Crusade may seem jokey and light at times, but they had a core of mystery to them still. Also, personally, don't make Mutt the lead character...ideally not even include him..for the sake of it. Though, I am guessing he'd HAVE to appear now... Indy always has altering sidekicks, his family doesn't need to be dragged on all his adventures.
George now has the alien thing out of his system he has wanted since 1995-ish. So, possibly, we could have some other religious artifact. I don't mind the alien theme at all, all the Indy movies vary, and I think CS could have been "excellent" with the others if handled right.