Trust me, as Bill Clinton says "I feel your pain", but from what I see in the examples you specify, a lot of the pain may very well be from the process you take. No saying it's you but a lot of people that come from other software tend to, by human nature, force the software they are on to act just like the one they are used to using...if that makes sense. Again, that may or may not be the case here.
But I really, really have to disagree with the claim of "Inventor doesn't understand the need of engineers who design from scratch or do things on the fly." Sorry, but I find that statement to be extremely incorrect. If anything it's the complete opposite of what you state. First and foremost, unlike SW, Inventor doesn't dictate you workflow. You can design in Inventor in any approach you care to. Top-down, bottom-up, middle-out. A vast majority of what I've done in Inventor has been basically "on the fly" and never had much of an issue in the process. Maybe we simply approach things differently? Have you tried using Fusion or its functions in Inventor? How about using Relax mode, do you use the Design Generator tools, the analysis tools, Simulation tools, etc.? There's numerous ways/commands in Inventor to do what I refer to as "what-ifs". And this is not meant as any kind of insult and frankly I don't know why people tend to take it as one, but have you had formal training in Inventor? And by "Formal" I mean by Adesk or one of their better resellers? And by better, I mean there are resellers out there that frankly don't know their arse from the elbow when it comes to training. I've had to "cleanup" their training messes on numerous occasions. I'd suggest someone like Imaginit or Ketiv.
For example, the derived part issue you pointed out, the "ballache" seems to be more the process that you have your files scattered all over the place. I'll have to assume you don't use Vault. Even if you do, why are your files all over the place? Would it help any if you had the part needed already open? I find this issue along the lines of when I have one of my guys detailing a part/assy and they have to navigate to such part when they go to create that first view. Once I informed them that if the file is open in Inventor, the file reference in the view command will default to it or if multiple files are open, you simply select the one you want in the pull down. None of them knew such and guess what? All that complaining has gone away now.
As far as the Transparency tool in Inventor, I have to agree with whoever said they feel it's done correctly in Inventor, for the simple fact that in real word, if a part is transparent, it's still there, you can't simply reach thru it and grab the item behind it. The next time you're walking down the street in front of a store and try to grab the display items...can't do it. Thus in Inventor, in order to do such, you use the "enable/un-enable" command. To me that just makes sense. There are a number of approaches to be able to work with parts that are buried in an assembly in Inventor, I've listed a few of them previously, I just don't see what the issue is. I've had no problem doing such in assemblies of engines to aircraft and I can't recall the times I've actually used the "enable" command to do such. I honestly do not see what the fuss is about other than people trying to force Inventor to be more like SW.
Again, I don't want to get into a peeing match here because just as you can posts numerous examples of how Inventor can't do something, or does it wrong in your opinion, I can do the very same thing for SW. And as far as proving how Inventor is leading the pack, well I can very easily do that by simply using SW's own published info as proof. But again, this is not the place. My main contention is, Inventor should improve issues it needs to improve (same with SW and any other cad package out there), but to claim it needs to be just like its competitor? No, sorry, again, that's like demanding Ford change their trucks to be just like Chevy.