Hi bro,
Actually cisco uses GRE over IPSEC for routing trafffic to be tunneled bcs through IPSEC only unicast traffic can pass, not broadcast or multicast so routing traffic can not pass through IPSEC tunnel, so solution is that first tunnel multicast/broadcast ip payload (like routing protocol traffic) in GRE tunnel to make it unicast and then encrypt it via IPSEC tunnel.
But on juniper firewalls IPSEC tunnel can pass routing traffic so no need to make GRE over IPSEC tunnel to pass routing protocol traffic between two Juniper firewalls.
Now cisco also support route based VPN which can pass routing traffic through IPSEC VPN with out help of GRE. The sample configuration of route based VPN is below:
RTRA(config)# crypto isakmp policy 10
RTRA(config-isakmp)# encryption 3des
RTRA(config-isakmp)# hash sha
RTRA(config-isakmp)# authentication pre-share
RTRA(config-isakmp)# group 2
RTRA(config-isakmp)# exit
RTRA(config)# crypto isakmp key cisco123 address <public IP of ISG> 255.255.255.255 no-xauth
RTRA(config)# crypto ipsec transform-set RTRtran esp-aes esp-sha-hmac
RTRA(cfg-crypto-trans)# exit
RTRA(config)# crypto ipsec profile VTI
RTRA(ipsec-profile)# set transform-set RTRtran
RTRA(ipsec-profile)# exit
RTRA(config)# interface tunnel 0
RTRA(config-if)# ip address 192.168.3.1 255.255.255.0
RTRA(config-if)# tunnel source <WAN IP at cisco side>
RTRA(config-if)# tunnel destination <WAN IP of ISG>
RTRA(config-if)# tunnel mode ipsec ipv4
RTRA(config-if)# tunnel protection ipsec VTI
-For routing traffic passed through u should enable routing protocol like OSPF on tunnel interface not WAN interface
Hope this helps
Thanks