Venom, at least, got some development; in fact, I'd say it was Sandman who was short-shrifted in that film. Both the black suit and Topher Grace's character had a goodly amount of screen time; only after the two melded did things seem to speed up uncontrollably. Phoenix, on the other hand, remained a cipher throughout the film, killing loved ones and allying herself with Magneto seemingly without reason, never really interacting with other characters given the autistic portrayal... Yes, definately the Phoenix was the storylined that failed the most to live up to its potential.
Also, Venom might be getting his (its?) own spinoff, whereas I think we've seen all of Phoenix we're ever going to see, barring some reboot many years down the line...
Fictitiously yours, Trent Roman