Here the good document on L2 Security -VLAN Security White Paper You can find answer on your question and many others there.
Lets consider this document and find answer on your question. There are two main reasons to take in account when choosing vlan to use as native:
1) Dont use vlan 1 as native because
The reason VLAN 1 became a special VLAN is that L2 devices needed to have a default VLAN to assign to their ports, including their management port(s). In addition to that, many L2 protocols such as CDP, PAgP, and VTP needed to be sent on a specific VLAN on trunk links. For all these purposes VLAN 1 was chosen.
As a consequence, VLAN 1 may sometimes end up unwisely spanning the entire network if not appropriately pruned and, if its diameter is large enough, the risk of instability can increase significantly. Besides the practice of using a potentially omnipresent VLAN for management purposes puts trusted devices to higher risk of security attacks from untrusted devices that by misconfiguration or pure accident gain access to VLAN 1 and try to exploit this unexpected security hole.
To redeem VLAN 1 from its bad reputation, a simple common-sense security principle can be used: as a generic security rule the network administrator should prune any VLAN, and in particular VLAN 1, from all the ports where that VLAN is not strictly needed.
2) Choose unused vlan as native to prevent vlan-hopping (double-encapsulated attack):
When double-encapsulated 802.1Q packets are injected into the network from a device whose VLAN happens to be the native VLAN of a trunk, the VLAN identification of those packets cannot be preserved from end to end since the 802.1Q trunk would always modify the packets by stripping their outer tag. After the external tag is removed, the internal tag permanently becomes the packet's only VLAN identifier. Therefore, by double-encapsulating packets with two different tags, traffic can be made to hop across VLANs.
This scenario is to be considered a misconfiguration, since the 802.1Q standard does not necessarily force the users to use the native VLAN in these cases. As a matter of fact, the proper configuration that should always be used is to clear the native VLAN from all 802.1Q trunks (alternatively, setting them to 802.1q-all-tagged mode achieves the exact same result). In cases where the native VLAN cannot be cleared, then always pick an unused VLAN as native VLAN of all the trunks; don't use this VLAN for any other purpose. Protocols like STP, DTP, and UDLD (check out [3]) should be the only rightful users of the native VLAN and their traffic should be completely isolated from any data packets.
Regards,
