Crystal Skull's problems weren't related to Ford's age, or Spielberg, or even the ancient aliens idea (for all of the flak Lucas gets, I do understand his wish to make a spin on B-movie sci-fi with Indiana Jones in the atomic age). Crystal Skull was weak because of the script.
This.
There was no sense of wonderment. No sense of discovery or exploration. No sense of peril. They found the dang skull in the first hour of the film, and they faced precious-little danger in doing so. Finding the jungle city was like rather pedestrian...it was like they said "Okay, we've been working on this idea since 1993 and the script has been worked on in various forms since 1997. If we're going to do this, let's just go with THIS script. We aren't going to rewrite it yet again."
The script was a paint-by-numbers, horrendous thing with Indiana Jones elements just thrown together. I did enjoy the first half-hour, but the film just fell apart once they reached Peru.
Karen Allen's acting was rather forced and awkward...maybe you could blame Spielberg there. Maybe you could blame Lucas for the CGI groundhogs. But I don't think it was incompetently directed at all. There's only so much a director can do with a weak script.
I would also argue the script was laden with nostalgia.
Get rid of all the trappings, nods, winks, etc. Just tell a story.