The Sankara Stones lack the gravity of the Ark or the Grail but the stakes of the rescuing the children and the menace of Mola Ram made up for it. His whole "We will rule the world" spiel may be outlandish but at least he could back up the threat with actual black magic; by this point in the film we've seen him brainwash a number of people and cause a guy's heart to burst into frame. Plus he's actually scary.
Spalko gets a similar speech but there's no reason to believe the skull can actually be harnessed, and the movie makes the weird choice to undermine her paranormal abilities from the opening scene, to the point where we're left to wonder if she even has them in the first place. So she just kind of comes off as a crackpot who is a danger to herself more than to the heroes, which proves to be the case. And because Spalko's most ruthless actions happen off-screen and are carried out by her henchman, she's deprived of a real villainous moment, which even Donovan had.
I think a weak villain wouldn't have been as much a liability if the film had raised the stakes in other areas, but it consistently refuses to do so. The most egregious example is the whimper with which it initiates the third act. Indy proceeds to the lost city because the skull tells him to. That's it. It's a complete cop-out that the skull drives Oxley mad but affects Indy just enough that he can hear its commands but not actually suffer ill-effects. Imagine if Indy was losing his sanity and they had to return the skull to restore it. That would give the journey into Akator some urgency in the same way that shooting Connery turned up the heat on the Three Trials.