L2TP is Layer 2 tunneling protocol. EoIP is ethernet over IP. L2TP also works over IP. Ethernet is Layer 2. So according to name it's the same. Both support IPSec encryption in MT, so... What's the difference basically? I'm talking from site-to-site bridging perspective. Lets say I have 2 sites and I want to bridge 2 networks on each of them on L2 with IPSec (including broadcasts and stuff, completely transparent bridge) what would be more suitable and why?

If i understand correctly I'd need to create 2 EoIP interfaces with different tunnel IDs, give some IPSec policy and simply bridge them. Or 1 EoIP and use VLANs on it. With L2TP create server and client then enable BCP and some IPSec policy as well, then some VLANs? I guess? So what's the difference? Are they like really close alternatives just like GRE and IPIP? If so then what are advantages of each of them?

L2TP is normally (also in MikroTik) used to tunnel PPP over IP, so it will have user/password authentication and
will transport IP with a single IP address at the client side. EoIP transports raw ethernet frames. That can be done
with standard L2TP as well, but I don't think it can be done in a MikroTIk router.

To really bridge 2 networks (bad plan!) you would use EoIP.
In reality I would use GRE over IPsec to make a link that can then route IP using static routes or a routing protocol.
It won't transport all-hosts broadcasts but it can transport directed broadcasts.

Why bridging 2 networks is bad plan? I mean well yeah it is kind of bad plan if it's like over an internet because you could easily hog link, but if there's relatively high speed link between them then well why not? Also I have IP firewall on bridge enabled, configured to consider traffic between bridge ports so I don't think it involves any serious security issues.

Besides EoIP in MT (at least if used with IPSec) uses GRE, i had to open ports in fw to allow that.

Normally when you "need" broadcasts between two dislocated networks it is an indication of bad network design.
But don't let me hold you back, it is not my network

I have an RB750 tunneled to a 751 using EOIP with L2TP.

One Mikrotik is 192.168.100.2, the other is 192.168.100.10. I started out using 192.168.200.x for my second site but could not make it work.

EOIP lets me access PCs on the network by their name, ie \\acer2\c, where L2TP from a laptop on a motel wifi needs \\192.168.100.25 to see the PC.