[HTC One SV] TVTV:
Well, yes, all Android phones i know of use this kind of partitioning. That's because Android is based on Linux and runs best on Linux partitions (for various reasons: speed, reliability, security etc.). Thus all of the system-available partitions (system, app, cache etc.) are Linux partitions. But Linux partitions cannot be accessed by a Windows computer (at least not out of the box). That's why phone memory and SD memory are Windows partitions, so that your phone would be "seen" by Windows as an USB stick, in order for you to be able to transfer files to and from it without the need for additional software, such as Apple uses (the dreaded iTunes).

So, there you go. That's the main reason why we can't have one huge partition for apps, games, music etc. like the iPhone does. My firm belief is that they also use this as a marketing trick. You buy a more expensive phone, you get more phone memory and more app storage space (for example, the Galaxy S2 has a huge 2 GB of app space, as it was once a flagship phone). :)

Quick tip: Go to Settings -> Apps and "click" on the On Phone Storage tab. Every app that you see there can be moved to phone memory. If it's already on phone memory, it will have a check mark next to its name. If it's not, it won't. In order to move an app to phone memory, thus clearing space on the app partition, you will have to click on an app's name, then click the Move tab on the app's properties screen.

Remember: if an app has widgets and is moved to phone memory (that's if the dev allows it in the first place, and many don't), the widgets won't be available anymore.

In terms of system updates and the system partition, well, yes, some phones won't get updated past a certain point because the updates would be too large for their system partition's size. Their partition table would have to be altered and that can only be done by running a RUU or using a specialized piece of software, with the phone connected to the computer via USB cable (OTA - over the air - updates cannot do this). This process is very dangerous and would cause the destruction of all user data on the phone. The danger lies in the fact that if anything goes wrong (computer reboots all of a sudden, an anti-virus software interferes with the RUU utility, the phone runs out of battery, the user accidentally disconnects the cable etc.), the phone might end up bricked. And manufacturers aren't usually prepared to take such a risk, for reasons which are easy to understand.

Thankfully, our device has some 2+ GB of system space, which should be enough for Sense 5 on WVGA screen res. :)

As for an update crafted specifically for advanced users, that wouldn't fly, because less experienced/tech savvy users would still try it then complain about HTC's methods and that they have lost all of their data etc. In today's world it's all or nothing. Example: One S users who bought the S4 variant might not get 4.2.2 because One S users who bought the S3 variant can't get it (driver issues - Qualcomm has decided to drop support for the S3 SoC on Android versions above 4.1) and if only some One S users would get the update, it would look bad, very-very bad, for HTC.