Cisco - if you pay for it - will always have better support. Its also understandably got more documentation (official and user made) and bigger 'community' of users to get answers from.
Cisco is generally also very stable.
Mikrotik is different. If you research, configure, test and deploy properly, they can be solid. We moved from Cisco 7200's at the core to 2x Mikrotik CCR1036's at the core. It gave us redundancy for a price less than half of a single Cisco unit to give equivalent performance. I was lucky to have been using Mikrotik's for WISP applications before the CCR series, so it was an OK move for me in a knowledge stand-point.
Mikrotik support can be attentive and generally keen to help figure out issues (so they can fix for next software release), but one major annoying part is the release cycle and the requirement to always upgrade for support. Part of researching and ensuring stability in a network is software selection, making sure certain versions don't have any major bugs for features you'd like to use, so being told you need to upgrade and possibly have exposure to an introduced bug can be quite painful.
All-in-all, its a cost benefit vs risk deal. If you have high margin product, and can afford Cisco, it should never break, if you are like most ISP's and margins a low, Mikrotik definitely a good option to investigate.