Certificate tokens and OTP tokens are similar to a degree, but in practice, their implementations are very different.
I would describe in summary as such:
OTP - light-weight, point solution, easier, proprietary integrations. Less secure, less interoperable, higher cost per authenticator
Certificate/PKI - heavy-duty, broad solution, extremely interoperable, multi-use, usable for physical and logical access
A more detailed description follows
OTP
- Standard basis: Proprietary generally, OSS solutions may exist
- OTP authenticator cost: 25 - 150 per unit + server software
- integration level of effort: low
- integration: limited to covered products (not many)
- OSS friendly: no
- Proprietary: yes
- interoperable with partners or govts: no
- usable for PACS: no
- usable for LACS: yes
- usable as an ID: no known token IDs.
- usable for file storage: no
- security level: moderate
- token duplication for backups: possible but never seen
- server tokens: believed not to exist
- usable by autonomous enterprise applications for machine to machine: no
- form factors: very limited
- easily usable with commandline apps: no
- hooks for applications: very limited, if any.
- software implementations: no
- hardware implementations: only
- customizing: little/none
- integration with air-gaps: no
- integration with stand-alone computers: no
- middleware required: no
- 3rd party validation client recommended/required: no
- reader driver needed: no
- control via Active Directory / GPOs: minimal
- interoperability with mobile devices: rarely, if supported
Certificate / PKI
- Standard basis: x509 PKI, along with published RFCs, commercial & OSS implementations
- OTP authenticator cost: 5 - 35 per unit + server software
- integration level of effort: low
- integration: almost unlimited; I count 200+ integration use cases in my agency.
- OSS friendly: yes
- Proprietary: no
- interoperable with partners or govts: yes
- usable for PACS: yes
- usable for LACS: yes
- usable as an ID: yes
- usable for file storage: yes
- security level: high
- token duplication for backups:: possible via secure means
- server tokens: exist in many form factors
- usability by autonomous enterprise applications for machine to machine: yes
- form factors: extremely scalable, a multitude of devices
- easily usable with commandline apps: yes
- hooks for applications: exist for many applications
- software implementations: yes
- hardware implementations: yes
- customizing: extensive
- integration with air-gaps: yes
- integration with stand-alone computers: yes
- middleware required: yes
- 3rd party validation client recommended/required: yes
- reader driver needed: occasionally, mainly for old operating systems
- control via Active Directory / GPOs: extensive
- interoperability with mobile devices: automatic rekeying supported with iOS & Android
OTP challenges:
I have seen many an OTP implementation where users are still required to use an OTP token for authentication events, but then have to drop to an additional software certificate system for encrypted email. This leads to insecure situations and an OTP is less user friendly. Because OTPs have so few integration points, they are usable mainly as a point solution when compared to a PKI.
Certificate/PKI challenges:
Much of this comes down to good planning, and a robust PKI implementation. When you are talking a full enterprise PKI, you are talking a large amount of infrastructure. See my post at https://serverfault.com/a/377230/40488 for good examples of the amount of infrastructure we are talking about. Although a PKI is thought of as expensive, there are companies that can run this for a business as an outsourced service cheaper than you can stand it up. Also, you are wedded to the x509 standard so it might be a good idea to read up Guttman's writings on the subject.
Conclusion:
I would recommend you make your decision for which authenticator based on the amount of integration points.
If you are heading towards just using it for VPN logon and Windows logon, and a few application authentications only, an OTP might be better.
If you are looking for VPN logon, Windows logon, secure email (SMIME), cloud based applications, full-disk encryption, usage with command line utilities, SSH, and extensive integration with OSS products, tie-ins to your MDM solution for mobiles, or potential re-use as an ID badge or physical access token, or regulated industries, or govt type of work where security is paramount, I'd go with the Certificate/PKI system in one of the many smartcard form factors.