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Of the two, it would appear that Unicorn was the more useful ship, having been designed and built from the keel up as an aircraft depot ship which was nevertheless able to act as a carrier if necessary Unicorn's TROM (http://www.naval-history.net/xGM-Chrono-04CV-Unicorn.htm) gives her speed as 22 knots rather than 24, which would make her a tad slow to be operating with real fleet carriers. But then the Combined Fleet page and other sources I have seen indicate that Junyo never made more than 22-23 knots in service, and had unreliable machinery to boot. I seem to remember some restrictions on Junyo's flight operations due to the size of her elevators or her speed or both, but I'm not sure of that. Unicorn is reported to have been equipped with elevators large enough to accommodate any kind of aircraft in naval service at the time she was built. Certainly Unicorn seems to have been the more robust ship, having had her repair facilities refitted in 1955, although she was in reserve at the time. I doubt, even if the IJN had survived the war, that Junyo would have been retained much beyond 1945.

Junyo supposedly could operate more planes, but practically speaking, I think the two vessels were about equal in the number of aircraft which they could launch in a single strike. My impression is that Unicorn was much better equipped with aircraft repair and handling facilities than Junyo. If you are thinking in terms of a one-on-one match-up, my opinion is that the edge definitely goes to Unicorn.