I agree with a lot of this but I think it is easier said than done. Since WWOHP the expectations of guests have surged. They can’t build lands like old Fantasyland or Frontierland anymore. I’m not saying there isn’t waste, there is a ton of it. But the cost of building quality attractions for the parks (Pandora, SWGE) has increased with guest expectations. EE was $100 million but that attraction is the exception for Disney, not the rule. Disney has always gone over budget. Look at DL’s construction back in 1955. The final cost was astronomical compared to the initial budget. Look at EPCOT Center. I wish they could crank out EE caliber attractions at that price but it is not easy. Disney has put in a ton of effort into the parks since 2010, and they should be commended for that. They haven’t been perfect. As such, I hope that this change in leadership leads to better things for the parks, guest, cast and company.
The cost of Everest doesn't get brought up because it was a particularly frugal project. On the contrary, Everest gets used as a benchmark because the $100 million budget was mind-bogglingly lavish for a theme park attraction at the time (though I believe after its overruns, Mission:Space ended up in that same ballpark a few years prior).
If you go back and check out some of the attraction's pre-opening media, it's easy to see how big and extravagant the whole thing was. Research expeditions to Nepal! A detailed mythology to be explained in the queue 'museum'! An expansion of the park's physical size with a whole new sub-section of Asia! Three intertwined-but-separate structures! An animatronic with the thrust of a 747!
And yet, just 5 years later, WDI was spending the same amount on a pretty straightforward book report dark ride of an animated movie, whose development costs were shared between two locations, and required tens of millions more to properly finish a few years later. I remember hearing $70M thrown around for WWOHP, though I'm not sure whether that was for the whole land or just Forbidden Journey; regardless, it shows that competitors can build WDI-caliber additions for a fraction of the price.
These days, it seems like even a simple flat ride from WDI is approaching the once-mind-boggling price of $100M, while the starting price for an E-ticket is $250M. And let's not even talk about the cost of Cosmic Rewind, either in terms of dollars or lost future opportunities for the park.
To your point about going over budget, it's actually rare that projects go significantly over once the budget has been approved. Sure, overruns may cause some scope reductions (dark rooms in Indiana Jones Adventure, attraction pads left for future expansion), but its rare for new projects to require large additional sums of money. Once the wheels are in motion, the bank isn't going to increase the funding without serious scrutiny. Even your examples of the original builds on DL and EPCOT Center mostly stuck to their approved budgets, though both required additional investments in their first few years of operation to keep up with demand.
Was Everest a good return on investment, in the sense that it brought a lot more guests/spending to the park for its price? Yes, it's one of the best examples of that. Was it a low-budget attraction? Absolutely not. And that it seems inexpensive today shows how much WDI's costs have spiraled out of control in recent years.