This post explains you the major difference between VMFS 5 datastore upgrade from VMFS 3 and  newly created VMFS 5 datastore. VMFS 5 is available as part of vSphere 5. VMFS 5 is introduced with lot of performance enhancements. Newly installed ESXi 5 will be formatted with VMFS 5 version but if you have upgraded the ESX 4 or ESX 4.1 to ESXi 5, then datastore version will be VMFS 3 only. You will able to upgrade the VMFS 3 to VMFS 5 via vSphere client once ESXi upgrade is Complete. Even though the upgraded datastore will be with VMFS 5 version  but there are many technical difference between upgraded VMFS 5 and newly created VMFS 5. This posts tells you some major differences between upgraded VMFS 5 and  newly created VMFS 5.

Capabilities	Upgraded VMFS 5	Newly Created VMFS 5
Max datastore size	64 TB	64 TB
Maximum size of RDM in Physical Compatibility	64 TB	64 TB
Block Size	Continuous to use the previous block size which may be 1MB/2MB/4MB/8 MB	only 1 MB block size
Sub-block size	64 KB sub-blocks	8 KB  sub-blocks
File limit	30,000	100,000
Partition Style	MBR (Master Boot Record) style	GPT (GUID Partition Table)
Partition Sector	partition starting on sector 128	partition starting on sector 2,048
Maximum size of RDM in Virtual Compatibility	2 TB  less 512 bytes	2 TB  less 512 bytes
Max size of file	2 TB  less 512 bytes	2 TB  less 512 bytes