Hi!

What kind of tunnel with encryption is better to choose to connect 2 or more branches for all kinds of traffic: file sharing, RDP, database. Traffic should be routed, not bridged.

Your best bet will be IPSEC or IPSEC with IPIP or similar.

My fried has replaced a pair of Cisco 1841 with pair or CCR1036 and users complains that the speed of interaction of their database applications has lowered.

Cisco was connected with IPSEC tunnel

interface Tunnel1
ip address 10.10.10.2 255.255.255.252
ip mtu 1400
ip tcp adjust-mss 1360
tunnel source 172.16.127.83
tunnel destination 172.35.84.194
tunnel mode ipsec ipv4
tunnel protection ipsec profile vpn1

and CCR routers was configured with simple ip tunnel even without any encryption. now he replaced an ip tunnel with l2tp tunnel and it becomes work faster.

advice please how to make an ipsec tunnel the way cisco do it?

That's hard to answer because Cisco doesn't have just one way to do IPSEC. All tunnels have some overhead and all tunnels have the potential to slow down a connection. IPSEC, as it relates to MikroTik, does perform differently on different Routerboards and with different RouterOS versions. We frequently use RouterOS 5.26 for IPSEC because it seems to be stable. When it comes right down to it, you are going to choose an IPSEC methodology, for whatever reasons are important to you, and then you are going to have to experiment until you find the right combination of hardware and software for what you need. There really is not a standard "one way" that works for everything.