This wasn't a case of 'reinventing the wheel' as I wrote the parser about 40 years ago, and it therefore predates systems such as Inform or TADS, although it has evolved a bit since then, particularly with the advent of QB64 which is very powerful, and a vast improvement on QBASIC. I much prefer writing my own code, as it gives me much more control over things.
I absolutely agree with the criticism of having to specifically TAKE [item] FROM [container] but that was just the way the parser was initially developed and I can't realistically see a way of getting round this without a complete re-write, which just isn't going to happen as I'm pushing 80 years of age.
'FLIP' switch was easy to fix as it merely involved inserting another verb synonym and took all of 30 seconds. Equally simple was coding round having to specify which key to use in each situation. The reason for not having done this initially was that in previous games more than one key could be present at the same time, although in Mortimer this is not the case. Both of these have been updated, although I haven't uploaded the new version as yet since I don't know if this is allowed while the Comp is still running (in any case, I can only update the Windows version).
There are some situations in the game where information is provided, such as when John leaves the cube on the table or when the message is displayed on the open trunk in the cellar. In all such situations information is clearly given on the screen, but if the player doesn't read this it could lead to them having to traipse all the way back. One exception to this is if you haven't exchanged the key prior to entering a location, such as needing the brass key in Florence, the bronze key in Runnymede or the iron key in Cambridge; you would then have to go back to the transmuter. I agree this could be a bit of a pain, so once a key has been used it's advisable to go back to the transmuter at the first opportunity.
One advantage of the unlimited inventory is that you should just take everything you are presented with, as you never know if you might need it or not.
Although there's no indication that you should go back to the rest room in Dallas once Oswald has left, I'd have thought that most players might have wondered if he'd left anything behind (as indeed he had :-) )