Development Hell: Quite a few stories got stuck in it or were vetoed altogether. One story would have seen the Eighth Doctor versus sentient paintings; another featured an earlier version of Izzy's character as a pair of twins Touched by Vorlons. The authors' notes really elaborate on the writing process, with plenty of first draft scans and hand-written notes. Alan Barnes ended up recycling his vetoed ideas for the Eighth Doctor in Charley Pollard's Big Finish story arc instead (notably in "Storm Warning" and "Neverland").
What Could Have Been: One potential comic would have been a multi-Doctor story, with Tenth meeting Eighth and Destrii.
Russell T Davies offered the actual Eight-Nine regeneration to the strip, but a variety of restrictions on the matter (not being able to feature the Ninth Doctor with anyone bar Rose, for example, and more importantly the whole Time War thing) led to the idea being ultimately dropped by the editorial staff, who felt they wouldn't be able to do it justice. A draft script and a drawing are available in the Eighth Doctor compilation The Flood.
They note in the commentary for Ninth Doctor compilation The Cruel Sea that they would've been de-canonised by "The Night of the Doctor" and the whole War Doctor thing.