MacOS – Upgrading OS slowing down machine

There are no disadvantages to a clean installation. But the return on Lion has been severely culled due to Apple's decision to prevent any kind of modification to the OS. With previous OS X builds, users were able to select (and deselect) packages (such as printer drivers, extended languages, etc.) during the installation process. Lion brings everything and the kitchen sink.

The ability to trim away parts of OS X was probably the most compelling reason to perform a clean install (saving GB of space).

Your notion of how hard drives work isn't accurate. There's no "prime" location for data, outer ring or inner ring. So long as the files are contiguous, your data will be delivered optimally. Access times depend on rotation latency (speed at which the disks spin, calculated in RPM) and seek times (the time it takes the head to reach the desired location to reach the file), although density plays a role too, by packing more bits of data per region (thus increasing throughput).

Moreover, OS X handles the defragementation of small files on a regular basis, ensuring continued performance over time. It's also of note that such things are gone by way of using SSDs.

Lastly, clean installations may also reduce bugs introduced by updates. While OS X is quite resilient, updates can introduce new bugs into the system. Often times, Apple technicians will request a clean installation and applying only the latest subsequent update in an attempt to isolate bugs (rather than upgrade from a previous version of the OS and then applying a slew of incremental updates). These problems are however quite rare.

I had to reformat the external drive I use for Time Machine. It said there was a permissions problem, that it was Read Only - which it wasn't, and a look at the Info for it confirmed it was Read & Write. Still, I just erased the drive and started again. Works fine now.