Hi,
OK, GRE(+IPSEC) is another point to point tunnelling protocol (it was first developed by CISCO),
you can also check this out: IPIP and EoIP in which they have similiar features.
http://wiki.mikrotik.com/wiki/Manual:Interface/Gre
GRE and IPIP are layer 3 tunneling protocols, in which you will need IP layer (IP address) and
thus routing protocols (including static routes are to be setup) to make the site to site VPN
tunnels workable.
L2TP interface however, is working on Layer 2 (imagine an Ethernet Switch), it does not bound by
the IP Layer, so we do not to worry about IP routing, so it is much more flexible and IP layer will
just work on top of Layer 2. It is even possible to create a VPN with a single subnet network
with DHCP and default gateway via L2TP.
Just a side note, if the main cetral hub has certain operational limitation (bandwidth, uptime,
etc), one thing to consider is to create a HUB site in the cloud, there is a new Mikrotic Cloud
Hosted Router (CHR) which is in the works right now.
http://forum.mikrotik.com/t/cloud-hosted-router/89979/1
regards,