The Janus Directive is one of the first story arcs I remember that had a uniform title banner and crossed over into multiple titles, without being a company-wide crossover. Checkmate and Suicide Squad were carrying some heat back then, so this story seemed like a big deal at the time. I didn't get to read the whole thing as it was coming out, and have yet to collect all of the issues so I can read it in its entirety. I think this would be a fun ride though.
I went with the Checkmate title, because Checkmate started off the arc, and because of all the titles involved, it has the highest visibility with today's fans. Plus, Suicide Squad was kind of a part of Checkmate at the time, so it wouldn't make sense to have that be the main title. For the cover, although I like Peacemaker on Suicide Squad #28, I'd go with the part 1 cover, from Checkmate #15. Going with the Checkmate title for the TPB, that makes more sense anyway.
Would you buy it? Let me know in the comments, and thanks for reading.