We've only seen Cobbs on the court, so I can't comment on Allen (if you've seen him somewhere, I'd love to hear your thoughts).
Rivals had both as 3-stars, while Scout gave them both two stars, so they're pretty similar in that regard (actually if you click on Cobbs profile on Rivals it lists "similar players" and one listed is Bryant Allen.)
Looking at their other offers, Cobbs had Iowa and USC as his most-high profile suitors, Allen had Kansas and Wisconsin. Advantage Allen, but with his football abilities it's hard to know how much that influenced teams.
If I had to guess, and it's just a guess, I'd say that Cobbs is a better basketball player right now but Allen is a better athlete. As far as potential, your guess is as good as mine.