If I have a very large space to cover in a large building with 2 different Mikrotik routers I'd like to know what some of the preferred method to set up would be.

Is WDS repeating still worth using?

Has anyone had success with the built-in mesh protocol?

Again, this is for an indoor application using the Mikrotik desktop routers.

Can you not working with network cables to connect the routerboards

As stated above, if you can wire them back to a switch, then simply set the units up to transmit the same SSID on different channels (1 and 11 say) and it will work fine.

If only one can be wired, then put them in AP-BRIDGE and use WDS. Mesh is not really applicable in this instance.