I agree with you on some level, that they do not leverage their own library enough, but what you don't see is that - if they relied simply on the Disney library, their audience considerably narrows.
And if your case rests on Peter Pan's Flight, it's pretty precarious - because Peter Pan's Flight has such lines because of tiny vehicles and the most antiquated loading procedure in the entire resort.
To answer your question about ToT - yeah, actually. Using a theme like Twilight Zone with that catchy theme music that everyone knows (even if you have never seen the show) immediately sets the tone of the pre-show (you always hear people start to get excited at that point). Could they have used something else? Yes (and originally, they were). But since Disney doesn't have any "creepy" franchises of their own, and certainly none known as well as the Twilight Zone brand, it made sense to make a partner.
And yeah, the original Star Tours would have sucked if it wasn't Star Wars-themed. They tried that - Body Wars. See how well that turned out (although it was cool because eventually it proved its value, it gave them spare parts to fix Star Tours until it finally got remodeled).
Let's face it, the problem is - if they didn't go to outside franchises, all we have are Disney animated films. The only live-action mega-success Disney has had has been PotC - which, ironically, is based on a ride to begin with. So I guess we could have ToT themed around Magica De Spell from Ducktales, or RnR based on The Party (go look that one up kids - I used to swear Damon was going to be my husband some day).
That said - I agree, we need more based on those classic Disney films - but to counter your "Peter Pan, case closed" - what are the most popular attractions at Disney world that have been built in the last 20 years? Most of them are not based on Disney franchises, or franchises that originated with Disney (and they bought them later).
As much as I love TLM ride, and wish we had a dozen more like it based on all the classic animated films - it's not exactly what makes national headlines and brings new blood into the parks, like something like a true Star Wars land just might do.