i'm having the exact same issue. I was able to use online upgrade process using vfont-d all the way up to ESXi 6.5 Update 1 (Security only) build 5969300 with out a problem.
I'm just 1 version update behind the full 6.5 U1 update.
When you look at the error output, it complains about a non zero exit status on one of the command executions.
Exception: /sbin/partedUtil getptbl /vmfs/devices/disks/mpx.vmhba32:C0:T0:L0 failed to execute: status(255)
Troubleshooting 101 says, attempt to run that execution myself and see what's going on.
[root@VMhost:/dev/disks] /sbin/partedUtil getptbl /vmfs/devices/disks/mpx.vmhba32:C0:T0:L0
Error: The device /dev/disks/mpx.vmhba32:C0:T0:L0 is so small that it cannot possibly store a file system or partition table. Perhaps you selected the wrong device?
Unable to get device /vmfs/devices/disks/mpx.vmhba32:C0:T0:L0
Okay so this is where it choked for sure.
The ESXI installer formats and makes multiple partitions on my USB drive where ESXi is running from which is typical.
Here's the lay out of my USB which is running build 5969300 just fine.
[root@VMhost:/dev/disks] ls -l | grep mpx.vmhba32
-rw------- 1 root root 18302628885633696256 Sep 10 20:11 mpx.vmhba32:C0:T0:L0
-rw------- 1 root root 4161536 Sep 10 20:11 mpx.vmhba32:C0:T0:L0:1
-rw------- 1 root root 262127616 Sep 10 20:11 mpx.vmhba32:C0:T0:L0:5
-rw------- 1 root root 262127616 Sep 10 20:11 mpx.vmhba32:C0:T0:L0:6
-rw------- 1 root root 115326976 Sep 10 20:11 mpx.vmhba32:C0:T0:L0:7
-rw------- 1 root root 299876352 Sep 10 20:11 mpx.vmhba32:C0:T0:L0:8
-rw------- 1 root root 2684354560 Sep 10 20:11 mpx.vmhba32:C0:T0:L0:9
lrwxrwxrwx 1 root root 20 Sep 10 20:11 vml.0000000000766d68626133323a303a30 -> mpx.vmhba32:C0:T0:L0
lrwxrwxrwx 1 root root 22 Sep 10 20:11 vml.0000000000766d68626133323a303a30:1 -> mpx.vmhba32:C0:T0:L0:1
lrwxrwxrwx 1 root root 22 Sep 10 20:11 vml.0000000000766d68626133323a303a30:5 -> mpx.vmhba32:C0:T0:L0:5
lrwxrwxrwx 1 root root 22 Sep 10 20:11 vml.0000000000766d68626133323a303a30:6 -> mpx.vmhba32:C0:T0:L0:6
lrwxrwxrwx 1 root root 22 Sep 10 20:11 vml.0000000000766d68626133323a303a30:7 -> mpx.vmhba32:C0:T0:L0:7
lrwxrwxrwx 1 root root 22 Sep 10 20:11 vml.0000000000766d68626133323a303a30:8 -> mpx.vmhba32:C0:T0:L0:8
lrwxrwxrwx 1 root root 22 Sep 10 20:11 vml.0000000000766d68626133323a303a30:9 -> mpx.vmhba32:C0:T0:L0:9
When it calls the drive with out a specific partition number, it returns no size and an error code as shown above. The individual partitions do however return a result just fine.
[root@VMhost:/dev/disks] /sbin/partedUtil getptbl /vmfs/devices/disks/mpx.vmhba32:C0:T0:L0:5
unknown
31 255 63 511968
[root@VMhost:/dev/disks] /sbin/partedUtil getptbl /vmfs/devices/disks/mpx.vmhba32:C0:T0:L0:6
unknown
31 255 63 511968
[root@VMhost:/dev/disks] /sbin/partedUtil getptbl /vmfs/devices/disks/mpx.vmhba32:C0:T0:L0:1
unknown
0 255 63 8128
This looks like a definitive logic bug to me that needs to be resolved by VMware. Either the version partedUtil getptbl is out of date and doesn't know how to deal with reading the disk with out a partition number or the installation script should be reading the individual partitions and not the disk identifier to get the size. A USB stick being 3GB or 300 GB will have no effect on an error like this so this is not a hardware requirement issue. It could be the USB stick and drive formatting is at fault but I don't think so. I decided to take a USB stick with a different ESXi installation on it and run the same partedUI command against the USB stick with out using the partition number and got the same error. I also got this error before upgrading to build 5969300 and the upgrade installer was able to read and upgrade to my USB stick just fine so i'm nearly positive this is a bug on the VMware side
If anyone knows a workaround to this or where else this should be posted to get the proper attention, I'm all ears.